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Conserved domains on  [gi|4504401|ref|NP_002110|]
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HLA class II histocompatibility antigen, DO alpha chain precursor [Homo sapiens]

Protein Classification

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List of domain hits

Name Accession Description Interval E-value
IgC1_MHC_II_alpha_HLA_DO cd21004
HLA class II histocompatibility antigen DO alpha; member of the C1-set of Ig superfamily (IgSF) ...
111-205 5.07e-74

HLA class II histocompatibility antigen DO alpha; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the nonclassical MHC class II (MHCII) protein, HLA-DO, which binds HLA-DM and influences the repertoire of peptides presented by MHCII proteins. In complex with HLA-DM, HLA-DO adopts a classical MHCII structure, with alterations near the a subunit's 310 helix. HLA-DO binds to HLA-DM at the same sites implicated in MHCII interaction, and kinetic analysis showed that HLA-DO acts as a competitive inhibitor by acting as a substrate mimic. Though more remains to be elucidated about the function of HLA-DO, its unique distribution in the mammalian body namely, the exclusive expression of HLA-DO in B cells, thymic medullary epithelial cells, and dendritic cells indicate that it may be of physiological importance and has inspired further research. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


:

Pssm-ID: 409595  Cd Length: 95  Bit Score: 220.07  E-value: 5.07e-74
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  111 VPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQ 190
Cdd:cd21004   1 VPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCK 80
                        90
                ....*....|....*
gi 4504401  191 VEHWGLDAPLLRHWE 205
Cdd:cd21004  81 VEHWGLDRPLLRHWE 95
MHC_II_alpha pfam00993
Class II histocompatibility antigen, alpha domain;
29-109 5.90e-40

Class II histocompatibility antigen, alpha domain;


:

Pssm-ID: 460019  Cd Length: 81  Bit Score: 132.70  E-value: 5.90e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401     29 DHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRA 108
Cdd:pfam00993   1 DHVGIYGCSFYQSYDPSGEYMFEFDGDELFYVDFKKKETVWRLPEFADFASFDPQGALANIAVCKNNLDILIKRSNSTPA 80

                  .
gi 4504401    109 I 109
Cdd:pfam00993  81 T 81
 
Name Accession Description Interval E-value
IgC1_MHC_II_alpha_HLA_DO cd21004
HLA class II histocompatibility antigen DO alpha; member of the C1-set of Ig superfamily (IgSF) ...
111-205 5.07e-74

HLA class II histocompatibility antigen DO alpha; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the nonclassical MHC class II (MHCII) protein, HLA-DO, which binds HLA-DM and influences the repertoire of peptides presented by MHCII proteins. In complex with HLA-DM, HLA-DO adopts a classical MHCII structure, with alterations near the a subunit's 310 helix. HLA-DO binds to HLA-DM at the same sites implicated in MHCII interaction, and kinetic analysis showed that HLA-DO acts as a competitive inhibitor by acting as a substrate mimic. Though more remains to be elucidated about the function of HLA-DO, its unique distribution in the mammalian body namely, the exclusive expression of HLA-DO in B cells, thymic medullary epithelial cells, and dendritic cells indicate that it may be of physiological importance and has inspired further research. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409595  Cd Length: 95  Bit Score: 220.07  E-value: 5.07e-74
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  111 VPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQ 190
Cdd:cd21004   1 VPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCK 80
                        90
                ....*....|....*
gi 4504401  191 VEHWGLDAPLLRHWE 205
Cdd:cd21004  81 VEHWGLDRPLLRHWE 95
MHC_II_alpha pfam00993
Class II histocompatibility antigen, alpha domain;
29-109 5.90e-40

Class II histocompatibility antigen, alpha domain;


Pssm-ID: 460019  Cd Length: 81  Bit Score: 132.70  E-value: 5.90e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401     29 DHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRA 108
Cdd:pfam00993   1 DHVGIYGCSFYQSYDPSGEYMFEFDGDELFYVDFKKKETVWRLPEFADFASFDPQGALANIAVCKNNLDILIKRSNSTPA 80

                  .
gi 4504401    109 I 109
Cdd:pfam00993  81 T 81
MHC_II_alpha smart00920
Class II histocompatibility antigen, alpha domain; Class II MHC glycoproteins are expressed on ...
31-110 3.79e-38

Class II histocompatibility antigen, alpha domain; Class II MHC glycoproteins are expressed on the surface of antigen-presenting cells (APC), including macrophages, dendritic cells and B cells. MHC II proteins present peptide antigens that originate extracellularly from foreign bodies such as bacteria. Proteins from the pathogen are degraded into peptide fragments within the APC, which sequesters these fragments into the endosome so they can bind to MHC class II proteins, before being transported to the cell surface. MHC class II receptors display antigens for recognition by helper T cells (stimulate development of B cell clones) and inflammatory T cells (cause the release of lymphokines that attract other cells to site of infection).


Pssm-ID: 214913  Cd Length: 81  Bit Score: 128.13  E-value: 3.79e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401      31 MGSYGPAFYQS-YGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAI 109
Cdd:smart00920   1 VGTYGHIVYCSdYDPSGEYMFEFDGDELFYVDFDKKETVWRLPEFADFASFDYQGALADIAVCKANLDILIKRSNSTPAT 80

                   .
gi 4504401     110 N 110
Cdd:smart00920  81 N 81
C1-set pfam07654
Immunoglobulin C1-set domain;
115-196 1.35e-35

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 121.59  E-value: 1.35e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401    115 VTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPS---AEDVYDCQV 191
Cdd:pfam07654   1 VYVFPPSPEELGKPNTLTCLVTGFYPPDITVTWLKNGQEVTEGVKTTPPSPNSDWTYQLSSYLTVTPSdweSGDEYTCRV 80

                  ....*
gi 4504401    192 EHWGL 196
Cdd:pfam07654  81 EHEGL 85
IGc1 smart00407
Immunoglobulin C-Type;
128-199 3.32e-28

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 102.39  E-value: 3.32e-28
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 4504401     128 PNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPF---VPSAEDVYDCQVEHWGLDAP 199
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEVTEGVSTTDPLKNSDGTYFLSSYLTVpasTWESGDVYTCQVTHEGLKEP 75
 
Name Accession Description Interval E-value
IgC1_MHC_II_alpha_HLA_DO cd21004
HLA class II histocompatibility antigen DO alpha; member of the C1-set of Ig superfamily (IgSF) ...
111-205 5.07e-74

HLA class II histocompatibility antigen DO alpha; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the nonclassical MHC class II (MHCII) protein, HLA-DO, which binds HLA-DM and influences the repertoire of peptides presented by MHCII proteins. In complex with HLA-DM, HLA-DO adopts a classical MHCII structure, with alterations near the a subunit's 310 helix. HLA-DO binds to HLA-DM at the same sites implicated in MHCII interaction, and kinetic analysis showed that HLA-DO acts as a competitive inhibitor by acting as a substrate mimic. Though more remains to be elucidated about the function of HLA-DO, its unique distribution in the mammalian body namely, the exclusive expression of HLA-DO in B cells, thymic medullary epithelial cells, and dendritic cells indicate that it may be of physiological importance and has inspired further research. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409595  Cd Length: 95  Bit Score: 220.07  E-value: 5.07e-74
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  111 VPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQ 190
Cdd:cd21004   1 VPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCK 80
                        90
                ....*....|....*
gi 4504401  191 VEHWGLDAPLLRHWE 205
Cdd:cd21004  81 VEHWGLDRPLLRHWE 95
IgC1_MHC_II_alpha cd05767
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of ...
111-205 9.43e-63

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of the major histocompatibility complex (MHC) class II alpha chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are also expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409424  Cd Length: 95  Bit Score: 191.37  E-value: 9.43e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  111 VPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQ 190
Cdd:cd05767   1 VPPEVTVFPKSPVELGEPNTLICFVDNFFPPVINVTWLRNGQPVTDGVSETVFLPREDHSFRKFSYLPFTPSEGDIYDCR 80
                        90
                ....*....|....*
gi 4504401  191 VEHWGLDAPLLRHWE 205
Cdd:cd05767  81 VEHWGLEEPLLKHWE 95
IgC1_MHC_II_alpha_HLA-DQ cd21008
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of ...
113-205 2.30e-55

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) DQ and related proteins; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) DQ. MHC class II molecules are encoded by three different loci, HLA-DR, -DQ, and -DP, which are about 70% similar to each other. HLA-DQ (DQ) is a cell surface receptor protein found on antigen presenting cells. It is an alphabeta heterodimer of type MHC class II. The alpha and beta chains are encoded by two loci, HLA-DQA1 and HLA-DQB1, that are adjacent to each other on chromosome band 6p21.3. A person often produces two alpha-chain and two beta chain variants and thus 4 isoforms of DQ. Two autoimmune diseases in which HLA-DQ is involved are celiac disease and diabetes mellitus type 1. DQ is one of several antigens involved in rejection of organ transplants. DQ8 is a split antigen of the DQ3 broad antigen. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409599  Cd Length: 95  Bit Score: 172.82  E-value: 2.30e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  113 PRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVE 192
Cdd:cd21008   3 PEVTVFPKSPVTLGQPNTLICLVDNIFPPVINITWLSNGHSVTEGVSETSFLSKSDHSFLKISYLTFLPSADDIYDCKVE 82
                        90
                ....*....|...
gi 4504401  193 HWGLDAPLLRHWE 205
Cdd:cd21008  83 HWGLDKPLLKHWE 95
IgC1_MHC_II_alpha_HLA-DR cd21007
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of ...
111-205 1.45e-50

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) DR; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) DR. MHC class II molecules are encoded by three different loci, HLA-DR, -DQ, and -DP, which are about 70% similar to each other. HLA-DR is a cell surface receptor protein found on antigen presenting cells. It is an alphabeta heterodimer of type MHC class II. The alpha and beta chains are encoded by two loci, HLA-DRA1 and HLA-DRB1, that are adjacent to each other on chromosome band 6p21.31. Susceptibility to multiple sclerosis and rheumatoid arthritis are associated with the human histocompatibility leukocyte antigen HLA-DR2 and HLA-DR4, respectively. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409598  Cd Length: 95  Bit Score: 160.60  E-value: 1.45e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  111 VPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQ 190
Cdd:cd21007   1 VPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCR 80
                        90
                ....*....|....*
gi 4504401  191 VEHWGLDAPLLRHWE 205
Cdd:cd21007  81 VEHWGLDEPLLKHWE 95
IgC1_MHC_II_alpha_I-EK cd21005
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of ...
111-205 2.76e-44

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) I-E; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) I-E. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409596  Cd Length: 95  Bit Score: 144.43  E-value: 2.76e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  111 VPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQ 190
Cdd:cd21005   1 VAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWLRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCE 80
                        90
                ....*....|....*
gi 4504401  191 VEHWGLDAPLLRHWE 205
Cdd:cd21005  81 VDHWGLEEPLRKHWE 95
IgC1_MHC_II_alpha_I-A cd21006
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of ...
113-204 1.42e-43

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) I-A; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) I-A. Three genetically distinct isotypes of class II MHC molecules are found in humans (HLA-DR, HLA-DQ, and HLA-DP), and two in mice (I-E and I-A). I-A and I-E molecules have the same basic features insofar as peptide loading and presentation, although each interacts with distinctly different sets of peptides. They also differ in that there is a relatively high incidence of deletion of the I-E a gene in both inbred strains of mice as well as wild mice and the lack of the reverse situation i.e. the deletion of I-A genes. A detailed structural understanding of the similarities and differences between I-A and the paralogous I-E could help illuminate the respective roles these molecules play in peptide presentation and T cell activation. Mouse I-Ag7 has a genetic susceptibility to autoimmune diabetes due to its small, uncharged amino acid residue at position 57 of their beta chain which results in the absence of a salt bridge between beta 57 and Arg alpha 76, which is adjacent to the P9 pocket of the peptide-binding groove. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409597  Cd Length: 95  Bit Score: 142.52  E-value: 1.42e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  113 PRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVE 192
Cdd:cd21006   3 PQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVTDGVYETSFLVNRDHSFHKLSYLTFIPSDDDIYDCKVE 82
                        90
                ....*....|..
gi 4504401  193 HWGLDAPLLRHW 204
Cdd:cd21006  83 HWGLEEPVLKHW 94
MHC_II_alpha pfam00993
Class II histocompatibility antigen, alpha domain;
29-109 5.90e-40

Class II histocompatibility antigen, alpha domain;


Pssm-ID: 460019  Cd Length: 81  Bit Score: 132.70  E-value: 5.90e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401     29 DHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRA 108
Cdd:pfam00993   1 DHVGIYGCSFYQSYDPSGEYMFEFDGDELFYVDFKKKETVWRLPEFADFASFDPQGALANIAVCKNNLDILIKRSNSTPA 80

                  .
gi 4504401    109 I 109
Cdd:pfam00993  81 T 81
MHC_II_alpha smart00920
Class II histocompatibility antigen, alpha domain; Class II MHC glycoproteins are expressed on ...
31-110 3.79e-38

Class II histocompatibility antigen, alpha domain; Class II MHC glycoproteins are expressed on the surface of antigen-presenting cells (APC), including macrophages, dendritic cells and B cells. MHC II proteins present peptide antigens that originate extracellularly from foreign bodies such as bacteria. Proteins from the pathogen are degraded into peptide fragments within the APC, which sequesters these fragments into the endosome so they can bind to MHC class II proteins, before being transported to the cell surface. MHC class II receptors display antigens for recognition by helper T cells (stimulate development of B cell clones) and inflammatory T cells (cause the release of lymphokines that attract other cells to site of infection).


Pssm-ID: 214913  Cd Length: 81  Bit Score: 128.13  E-value: 3.79e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401      31 MGSYGPAFYQS-YGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAI 109
Cdd:smart00920   1 VGTYGHIVYCSdYDPSGEYMFEFDGDELFYVDFDKKETVWRLPEFADFASFDYQGALADIAVCKANLDILIKRSNSTPAT 80

                   .
gi 4504401     110 N 110
Cdd:smart00920  81 N 81
C1-set pfam07654
Immunoglobulin C1-set domain;
115-196 1.35e-35

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 121.59  E-value: 1.35e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401    115 VTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPS---AEDVYDCQV 191
Cdd:pfam07654   1 VYVFPPSPEELGKPNTLTCLVTGFYPPDITVTWLKNGQEVTEGVKTTPPSPNSDWTYQLSSYLTVTPSdweSGDEYTCRV 80

                  ....*
gi 4504401    192 EHWGL 196
Cdd:pfam07654  81 EHEGL 85
IGc1 smart00407
Immunoglobulin C-Type;
128-199 3.32e-28

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 102.39  E-value: 3.32e-28
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 4504401     128 PNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPF---VPSAEDVYDCQVEHWGLDAP 199
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEVTEGVSTTDPLKNSDGTYFLSSYLTVpasTWESGDVYTCQVTHEGLKEP 75
IgC1_MHC_II_beta cd05766
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; member of ...
111-205 1.23e-24

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II beta chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes and they are also expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain has two globular domains (N- and C-terminal) and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409423  Cd Length: 96  Bit Score: 93.94  E-value: 1.23e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  111 VPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQ 190
Cdd:cd05766   2 VQPSVKVSPTKTGPLEHPNLLVCSVTGFYPAEIEVKWFRNGQEETAGVVSTELIPNGDWTFQILVMLETTPRRGDVYTCQ 81
                        90
                ....*....|....*
gi 4504401  191 VEHWGLDAPLLRHWE 205
Cdd:cd05766  82 VEHSSLQSPLTVDWR 96
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
114-204 2.23e-22

Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, classical Ig-like domains resembling the antibody constant domain. Members of the IgC1 family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, while the IgC domain is involved in oligomerization and molecular interactions. The structures in C1-set are smaller than those in the V-set; they have one beta sheet that is formed by strands A, B, E, and D and the other strands by G, F, C, and C'.


Pssm-ID: 409354  Cd Length: 95  Bit Score: 87.90  E-value: 2.23e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  114 RVTVL-PKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAED---VYDC 189
Cdd:cd00098   1 TVTLLpPSPEEKGGGKVTLVCLVSGFYPKDITVTWLKNGVPLTSGVSTSSPVEPNDGTYSVTSSLTVPPSDWDegaTYTC 80
                        90
                ....*....|....*
gi 4504401  190 QVEHWGLDAPLLRHW 204
Cdd:cd00098  81 VVTHESLKSPLSKTW 95
IgC1_MHC_II_beta_HLA-DR cd21000
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
111-204 3.05e-18

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DR; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DR. HLA-DR is an MHC class II cell surface receptor encoded by the human leukocyte antigen complex on chromosome 6 region 6p21.31. HLA-DR is also involved in several autoimmune conditions, disease susceptibility, and disease resistance including seronegative-rheumatoid arthritis, penicillamine-induced myasthenia, schizophrenia, Goodpasture syndrome, systemic lupus erythematosus, Alzheimers, tuberculoid leprosy, and Hashimoto's thyroiditis. HLA-DR molecules are upregulated in response to signaling. HLA-DR is an alphabeta heterodimer cell surface receptor, each subunit of which contains two extracellular domains, a membrane-spanning domain, and a cytoplasmic tail. Both alpha and beta chains are anchored in the membrane. The DR beta chain is encoded by 4 loci, however no more than 3 functional loci are present in a single individual, and no more than two on a single chromosome. Sometimes an individual may only possess 2 copies of the same locus, DRB1*. The HLA-DRB1 locus is ubiquitous and encodes a very large number of functionally variable gene products (HLA-DR1 to HLA-DR17). The HLA-DRB3 locus encodes the HLA-DR52 specificity, is moderately variable and is variably associated with certain HLA-DRB1 types. The HLA-DRB4 locus encodes the HLA-DR53 specificity, has some variation, and is associated with certain HLA-DRB1 types. The HLA-DRB5 locus encodes the HLA-DR51 specificity, which is typically invariable, and is linked to the HLA-DR2 types. Three genetically distinct isotypes of class II MHC molecules are found in humans (HLA-DR, HLA-DQ, and HLA-DP), and two in mice (I-E and I-A). MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409591  Cd Length: 96  Bit Score: 76.96  E-value: 3.05e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  111 VPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQ 190
Cdd:cd21000   2 VEPKVTVYPAKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQ 81
                        90
                ....*....|....
gi 4504401  191 VEHWGLDAPLLRHW 204
Cdd:cd21000  82 VEHPSVTSPLTVEW 95
IgC1_MHC_II_beta_HLA-DP cd21003
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
111-204 3.58e-18

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DP; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DP. HLA class II histocompatibility antigen, DP(W2) beta chain is a protein that in humans is encoded by the HLA-DPB1 gene. It plays a central role in the immune system by presenting peptides derived from extracellular proteins. MHC class II molecules are encoded by three different loci, HLA-DR, -DQ, and -DP, which are about 70% similar to each other. HLA-DP is an alphabeta heterodimer cell-surface receptor. Each DP subunit (alpha-subunit, beta-subunit) is composed of a alpha-helical N-terminal domain, an IgG-like beta sheet, a membrane spanning domain, and a cytoplasmic domain. The alpha-helical domain forms the sides of the peptide binding groove. The beta sheet regions form the base of the binding groove and the bulk of the molecule as well as the inter-subunit (non-covalent) binding region. Individuals carrying the MHCII allele, HLA-DP2, are at risk for chronic beryllium disease (CBD), a debilitating inflammatory lung condition caused by the reaction of CD4 T cells to inhaled beryllium. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409594  Cd Length: 96  Bit Score: 77.10  E-value: 3.58e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  111 VPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQ 190
Cdd:cd21003   2 VQPKVNVSPSKKGPLQHHNLLVCHVTDFYPGNIQVRWFLNGQEETAGVVSTNLIHNGDWTFQILVMLEMTPQQGDVYTCQ 81
                        90
                ....*....|....
gi 4504401  191 VEHWGLDAPLLRHW 204
Cdd:cd21003  82 VEHPSLDSPVTVEW 95
IgC1_MHC_II_beta_HLA-DQ_I-A cd21001
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
111-204 3.02e-17

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DQ and I-A; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of human histocompatibility antigen (HLA) DQ and mouse I-A. Three genetically distinct isotypes of class II MHC molecules are found in humans (HLA-DR, HLA-DQ, and HLA-DP), and two in mice (I-E and I-A). I-A and I-E have the same basic features insofar as peptide loading and presentation, they differ in that each interacts with distinctly different sets of peptides, and in the incidence of deletion of their genes. A structural understanding of the similarities and differences between I-A and I-E may help with understanding their roles in peptide presentation and T cell activation. Mouse I-Ag7 has a genetic susceptibility to autoimmune diabetes due to its small, uncharged amino acid residue at position 57 of their beta chain which results in the absence of a salt bridge between beta 57 and Arg alpha 76, which is adjacent to the P9 pocket of the peptide-binding groove. Human HLA-DR, -DQ, and -DP are about 70% similar to each other. HLA-DQ (DQ) is a cell surface receptor protein found on antigen presenting cells. It is an alphabeta heterodimer of type MHC class II. The alpha and beta chains are encoded by two loci, HLA-DQA1 and HLA-DQB1, that are adjacent to each other on chromosome band 6p21.3. A person often produces two alpha-chain and two beta chain variants and thus 4 isoforms of DQ. HLA-DQ is involved in the autoimmune diseases celiac disease and diabetes mellitus type. DQ is one of several antigens involved in rejection of organ transplants. DQ2 is encoded by the HLA-DQB1*02 allele group. DQ6 is encoded by the HLA-DQB1*06 allele group. DQ2 beta-chains combine with alpha-chains, encoded by genetically linked HLA-DQA1 alleles, to form the cis-haplotype isoforms. These isoforms, nicknamed DQ2.2 and DQ2.5, are also encoded by the DQA1*0201 and DQA1*0501 genes, respectively. DQ6 beta-chains combine with alpha-chains, encoded by genetically linked HLA-DQA1 alleles, to form the cis-haplotype isoforms. For DQ6, however, cis-isoform pairing only occurs with DQ1 alpha-chains. There are many haplotypes of DQ6. Susceptibility to Leptospirosis infection was found associated with undifferentiated DQ6. DQ8 is determined by the antibody recognition of beta8 and this generally detects the gene product of DQB1*0302. DQ8 is commonly linked to autoimmune disease in the human population. DQ8 is the second most predominant isoform linked to celiac disease and the DQ most linked to Type 1 diabetes. DQ8 increases the risk for rheumatoid arthritis and is linked to the primary risk locus for RA, HLA-DR4. DR4 also plays an important role in Type 1 diabetes. DQ8 is a split antigen of the DQ3 broad antigen. MHC class II molecules play a key role in the initiation of the antigen-specific immune response. They are expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice, and induced in nonprofessional APCs, such as keratinocyctes; they are expressed on the surface of activated human T cells and on T cells from other species. MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes; these peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC, and bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409592  Cd Length: 97  Bit Score: 74.38  E-value: 3.02e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  111 VPPRVTVLPkSRVE-LGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDC 189
Cdd:cd21001   2 VEPTVTISP-SRTEaLNHHNLLVCSVTDFYPGQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTC 80
                        90
                ....*....|....*
gi 4504401  190 QVEHWGLDAPLLRHW 204
Cdd:cd21001  81 HVEHPSLQSPITVEW 95
IgC1_beta2m cd05770
Class I major histocompatibility complex (MHC) beta-2-microglobulin; member of the C1-set of ...
111-205 1.17e-16

Class I major histocompatibility complex (MHC) beta-2-microglobulin; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin-like domain in beta-2-microglobulin (beta2m). Beta2m is the non-covalently bound light chain of the human class I major histocompatibility complex (MHC-I). Beta2m is structured as a beta-sandwich domain composed of two facing beta-sheets (four stranded and three stranded), that is typical of the C-type immunoglobulin superfamily. This structure is stabilized by an intramolecular disulfide bridge connecting two Cys residues in the facing beta-sheets. In vivo, MHC-I continuously exposes beta2m on the cell surface, where it may be released to plasmatic fluids, transported to the kidneys, degraded, and finally excreted.


Pssm-ID: 409427  Cd Length: 94  Bit Score: 72.90  E-value: 1.17e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  111 VPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQtVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQ 190
Cdd:cd05770   1 STPKVQVYSRFPAENGKPNVLNCYVSGFHPPDIEIRLLKNGV-KIEDVEQSDLSFSKDWTFYLLKYTEFTPTKGDEYACR 79
                        90
                ....*....|....*
gi 4504401  191 VEHWGLDAPLLRHWE 205
Cdd:cd05770  80 VRHNTLSEPKIYKWD 94
IgC1_MHC_II_beta_I-E cd20998
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
111-205 6.06e-16

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) I-E; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) I-E. Three genetically distinct isotypes of class II MHC molecules are found in humans (HLA-DR, HLA-DQ, and HLA-DP), and two in mice (I-E and I-A). I-A and I-E molecules have the same basic features insofar as peptide loading and presentation, although each interacts with distinctly different sets of peptides. They also differ in that there is a relatively high incidence of deletion of the I-E gene in both inbred strains of mice as well as wild mice and the lack of the reverse situation i.e. the deletion of I-A genes. A detailed structural understanding of the similarities and differences between I-A and the paralogous I-E could help illuminate the respective roles these molecules play in peptide presentation and T cell activation. Mouse I-Ag7 has a genetic susceptibility to autoimmune diabetes due to its small, uncharged amino acid residue at position 57 of their beta chain which results in the absence of a salt bridge between beta 57 and Arg alpha 76, which is adjacent to the P9 pocket of the peptide-binding groove. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409590  Cd Length: 99  Bit Score: 71.34  E-value: 6.06e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  111 VPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQ 190
Cdd:cd20998   5 VEPTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQ 84
                        90
                ....*....|....*
gi 4504401  191 VEHWGLDAPLLRHWE 205
Cdd:cd20998  85 VEHPSLTDPVTVEWK 99
IgC1_MHC_II_beta_HLA-DM cd21002
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
111-204 9.48e-14

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DM; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DM. Human HLA-DM plays a critical role in antigen presentation to CD4 T cells by catalyzing the exchange of peptides bound to MHC class II molecules. Type 1 diabetes is correlated with DM activation and it is also implicated in viral infections such as herpes simplex virus, celiac disease, multiple sclerosis, other autoimmune diseases, and leukemia. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409593  Cd Length: 97  Bit Score: 64.94  E-value: 9.48e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  111 VPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGV-AQTSFYSQPDHLFRKFHYLPFVPSAEDVYDC 189
Cdd:cd21002   2 RPPSVRVAPTTPFNTREPVMLACHVWGFYPADVTITWLKNGDPVAPHSsAPKTAQPNGDWTYQTQVTLAVTPSPGDTYTC 81
                        90
                ....*....|....*
gi 4504401  190 QVEHWGLDAPLLRHW 204
Cdd:cd21002  82 SVQHASLPEPLLEDW 96
IgC1_MHC_II_alpha_HLA-DM cd21009
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of ...
123-193 1.99e-12

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) DM; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) DM. Human HLA-DM, also known as H2-M in mice, plays a critical role in antigen presentation to CD4 T cells by catalyzing the exchange of peptides bound to MHC class II molecules. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409600  Cd Length: 94  Bit Score: 61.59  E-value: 1.99e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 4504401  123 VELGQPNILICIVDNIFPPVINITWLRNGQTVtEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEH 193
Cdd:cd21009  13 LEFGKPNTLVCFVSNLFPPMLTVNWQLHSVPV-EGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIVTH 82
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
112-200 7.98e-12

Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) light chain constant (C) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains.


Pssm-ID: 409496  Cd Length: 99  Bit Score: 60.16  E-value: 7.98e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  112 PPRVTVLPKSRVELgQPN--ILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFvpSAED---- 185
Cdd:cd07699   1 APSVTIFPPSSEEL-SSGkaTLVCLINKFYPGFATVTWKVDGSTVSSGVTTSKTEQQSDNTYSMSSYLTL--SSSDwnkh 77
                        90
                ....*....|....*.
gi 4504401  186 -VYDCQVEHWGLDAPL 200
Cdd:cd07699  78 kVYTCEVTHEGLSSTI 93
IgC1_CD1 cd21029
Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig ...
111-204 1.02e-09

Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin domain of Cluster of Differentiation (CD) 1. CD1 family of transmembrane glycoproteins, are structurally related to the major histocompatibility complex (MHC) proteins and form heterodimers with beta-2-microglobulin. They mediate the presentation of primarily lipid and glycolipid antigens of self or microbial origin to T cells. The human genome contains five CD1 family genes (CD1a, CD1b, CD1c, CD1d, and CD1e) organized in a cluster on chromosome 1. The CD1 family members are thought to differ in their cellular localization and specificity for particular lipid ligands. CD1a localizes to the plasma membrane and to recycling vesicles of the early endocytic system. Alternative splicing results in multiple transcript variants. Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I alpha chain. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. C1-set Ig domains have one beta sheet that is formed by strands A, B, E, and D and the other strands by G, F, C, and C'.


Pssm-ID: 409620  Cd Length: 93  Bit Score: 54.25  E-value: 1.02e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  111 VPPRVTVLPKSRVELGQpNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQ 190
Cdd:cd21029   1 VKPRVRLSSRPSPGDGH-LQLSCHVTGFYPRPIEVTWLRDGQEQMDGTQSGGILPNHDGTYQLRKTLDIAPGEGAGYSCR 79
                        90
                ....*....|....
gi 4504401  191 VEHWGLDAPLLRHW 204
Cdd:cd21029  80 VDHSSLKQDLIVYW 93
IgC1_Tapasin_R cd05771
Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; ...
113-200 8.97e-09

Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin-like domain on Tapasin-R. Tapasin is a V-C1 (variable-constant) immunoglobulin superfamily molecule present in the endoplasmic reticulum (ER), where it links MHC class I molecules to the transporter associated with antigen processing (TAP). Tapasin-R is a tapasin-related protein that contains similar structural motifs to Tapasin, with some marked differences, especially in the V domain, transmembrane and cytoplasmic regions. The majority of Tapasin-R is located within the ER; however, there may be some expression of Tapasin-R at the cell surface. Tapasin-R lacks an obvious ER retention signal.


Pssm-ID: 409428  Cd Length: 100  Bit Score: 51.73  E-value: 8.97e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  113 PRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLR---NGQTVTEGVAQTSFYSQPDHLFRKFH---YLPFVPSAED- 185
Cdd:cd05771   1 PRVRLSPKNLVKPDLPQTLSCHIAGYYPLDVDVEWLReepGGSESQVSRDGVSLSSHRQSVDGTYSissYLTLEPGTENr 80
                        90
                ....*....|....*..
gi 4504401  186 --VYDCQVEHWGLDAPL 200
Cdd:cd05771  81 gaTYTCRVTHVSLEEPL 97
IgC1_MHC_I_alpha3 cd07698
Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; ...
111-200 7.65e-08

Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I alpha chain. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409495  Cd Length: 92  Bit Score: 48.77  E-value: 7.65e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  111 VPPRVTVLPKSRVElGQPNiLICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLpFVPSAED-VYDC 189
Cdd:cd07698   1 DPPKVHVTHHPRSD-GEST-LRCWALGFYPAEITLTWQRDGEDQTQDMELVETRPNGDGTFQKWAAV-VVPSGEEqRYTC 77
                        90
                ....*....|.
gi 4504401  190 QVEHWGLDAPL 200
Cdd:cd07698  78 HVQHEGLPEPL 88
IgC1_MHC_Ia_RT1-Aa cd21015
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of RT1-Aa; member of the ...
112-205 1.96e-07

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of RT1-Aa; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of RT1-Aa. While most mammalian species transport these peptides into the ER via a single allele of TAP, rats have evolved different TAPs, TAP-A and TAP-B, RT1-Aa and RT1-A1c, which are associated with TAP-A and TAP-B. The rat MHC class Ia molecule RT1-Aa has the unusual capacity to bind long peptides ending in arginine, such as MTF-E, a thirteen-residue, maternally transmitted minor histocompatibility antigen. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409606  Cd Length: 95  Bit Score: 47.84  E-value: 1.96e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  112 PPR--VTVLPKSRVELgqpnILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDC 189
Cdd:cd21015   4 PPEahVTLHPRPEGDV----TLRCWALGFYPADITLTWQLNGEDLTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTC 79
                        90
                ....*....|....*.
gi 4504401  190 QVEHWGLDAPLLRHWE 205
Cdd:cd21015  80 RVEHEGLPKPLSQRWE 95
IgC1_MHC_Ia_HLA-B cd21026
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
112-205 3.42e-07

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) B and similar proteins; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) B and similar proteins. The classical class I molecules (HLA-A, -B, and -C) are responsible for the presentation of endogenous antigen to CD8+ T cells. The receptor is a heterodimer, and is composed of a heavy alpha chain and smaller beta chain. The alpha chain is encoded by a variant HLA-B gene, and the beta chain (beta-2-microglobulin) is an invariant beta-2-microglobulin molecule. The beta-2-microglobulin protein is coded for by a separate region of the human genome. Human leukocyte antigen (HLA) B*3501 (B35) is a common human allele involved in mediating protective immunity against HIV. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409617  Cd Length: 97  Bit Score: 47.50  E-value: 3.42e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  112 PPR--VTVLPKSRVELgqpnILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLpFVPSAEDV-YD 188
Cdd:cd21026   5 PPKthVTHHPISDHEA----TLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRTFQKWAAV-VVPSGEEQrYT 79
                        90
                ....*....|....*..
gi 4504401  189 CQVEHWGLDAPLLRHWE 205
Cdd:cd21026  80 CHVQHEGLPKPLTLRWE 96
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
113-202 4.30e-07

CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, and delta chains, and CH4 domain (fourth constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, epsilon, and mu chains; member of the C1-set of I; The members here are composed of the third and fourth immunoglobulin constant domain (IgC) of alpha, delta, gamma and alpha, epsilon, and mu heavy chains, respectively. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


Pssm-ID: 409425  Cd Length: 105  Bit Score: 47.33  E-value: 4.30e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  113 PRVTVLPKSRVELGQPN--ILICIVDNIFPPVINITWLRNGQTV-TEGVAQTSFYSQPDHLFRKFHYLPfVPSAE----D 185
Cdd:cd05768   1 PSVYLLPPPEEELSLNEtvTLTCLVKGFYPEDIFVSWLQNGEPLpSADYKTTAPVPESDGSFFVYSKLN-VSTADwnsgD 79
                        90
                ....*....|....*..
gi 4504401  186 VYDCQVEHWGLDAPLLR 202
Cdd:cd05768  80 VFSCVVGHEALPLQFTQ 96
IgC1_MHC_Ia_HLA-F cd21023
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
131-205 4.66e-07

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) F; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen alpha chain F (HLA-F). HLA-F, encoded by the HLA-F gene in humans, belongs to the non-classical HLA class I heavy chain paralogs. This class I molecule mainly exists as a heterodimer associated with the invariant light chain beta-2-microglobulin. HLA-F molecules can interact with both activating and inhibitory receptors on immune cells, such as NK cells, and can present a diverse panel of peptides. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409614  Cd Length: 98  Bit Score: 47.12  E-value: 4.66e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 4504401  131 LICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLpFVPSAEDV-YDCQVEHWGLDAPLLRHWE 205
Cdd:cd21023  22 LRCWALGFYPAEITLTWQRDGEEQTQDTELVETRPAGDGTFQKWAAV-VVPPGEEQrYTCHVQHEGLPQPLILRWE 96
IgC1_TCR_beta cd05769
T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig ...
112-177 7.56e-07

T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the T cell receptor (TCR) beta chain constant immunoglobulin domain. TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. This group includes the variable domain of the beta chain. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The antigen binding site is formed by the variable domains of the alpha and beta chains, located at the N-terminus of each chain. Alpha/beta TCRs recognize antigens differently from gamma/delta TCRs.


Pssm-ID: 409426 [Multi-domain]  Cd Length: 116  Bit Score: 46.60  E-value: 7.56e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  112 PPRVTVLPKSRVELGQPN--ILICIVDNIFPPVINITWLRNGQTVTEGVA--------QTSFYS-------------QPD 168
Cdd:cd05769   2 PPTVALFPPSEAEIRNKRkaTLVCLATGFYPDHVSLSWKVNGKEVKDGVAtdpqalreNTSTYSlssrlrvsatewfNPR 81
                        90
                ....*....|..
gi 4504401  169 HLFR---KFHYL 177
Cdd:cd05769  82 NTFTcivKFYGG 93
IgC1_MHC_1b_Qa-1b cd21820
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1b; member of the ...
112-212 9.54e-07

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1b; member of the C1-set of Ig superfamily (IgSF) domains; The non-classical mouse MHC class I (MHC-I) molecule Qa-1b is a non-polymorphic MHC molecule with an important function in innate immunity. It binds and presents signal peptides of classical MHC-I molecules at the cell surface and, as such, act as an indirect sensor for the normal expression of MHC-I molecules. This signal peptide dominantly accommodated in the groove of Qa-1b is called Qdm, for Qa-1 determinant modifier, and its amino acid sequence AMAPRTLLL is highly conserved among mammalian species. The Qdm/Qa-1b complex serves as a ligand for the germ-line encoded heterodimeric CD94/NKG2A receptors expressed on natural killer (NK) cells and activated CD8+ T cells and transduces inhibitory signals to these lymphocytes. Thus, upon binding, Qa-1b signals NK cells not to engage in cell lysis. The molecular basis of Qa-1b function is unclear.


Pssm-ID: 409625  Cd Length: 98  Bit Score: 45.91  E-value: 9.54e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  112 PPR--VTVLPKSRVELgqpnILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDC 189
Cdd:cd21820   5 PPKahVTHHPRSEDEV----TLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGTFQKWAAVVVPLGKEQYYTC 80
                        90       100
                ....*....|....*....|...
gi 4504401  190 QVEHWGLDAPLLRHWElqvpiPP 212
Cdd:cd21820  81 HVYHEGLPEPLTLRWE-----PP 98
IgC1_MHC_Ib_Qa-1 cd21013
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1 and similar ...
112-205 1.19e-06

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1 and similar proteins; member of the C1-set of Ig superfamily (IgSF) domains; Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1 and similar proteins. Qa-1 presents hydrophobic peptides including Qdm derived from the leader sequence of classical MHC I molecules for immune surveillance by NK cells. Qa-1 bound peptides derived from the TCR Vbeta8.2 of activated T cells also activates CD8+ regulatory T cells to control autoimmunity and maintain self-tolerance. Four allotypes of Qa-1 (Qa-1a-d) are expressed that are highly conserved in sequence but have several variations that could affect peptide binding to Qa-1 or TCR recognition. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409604  Cd Length: 97  Bit Score: 45.88  E-value: 1.19e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  112 PPR--VTVLPKSRVELgqpnILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDC 189
Cdd:cd21013   4 PPKahVTHHPRSEGYV----TLRCWALGFYPADITLTWQLNGEELTQDMEFVETRPAGDGTFQKWASVVVPLGKEQKYTC 79
                        90
                ....*....|....*.
gi 4504401  190 QVEHWGLDAPLLRHWE 205
Cdd:cd21013  80 HVEHEGLPEPLTLRWE 95
IgC1_MHC_Ia_HLA-G cd21022
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
131-204 4.00e-06

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) G; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) G. HLA-G histocompatibility antigen (also known as human leukocyte antigen G ; HLA-G) is a protein that in humans is encoded by the HLA-G gene. HLA-G belongs to the HLA nonclassical class I heavy chain paralogs. This class I molecule is a heterodimer consisting of a heavy chain and light chain, beta-2-microglobulin. The heavy chain is anchored in the membrane. HLA-G may play a role in immune tolerance in pregnancy, being expressed in the placenta by extravillous trophoblast cells (EVT), while the classical MHC class I genes (HLA-A and HLA-B) are not. Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I and class II. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. MHC class II molecules play a key role in the initiation of the antigen-specific immune repose. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409613  Cd Length: 94  Bit Score: 44.36  E-value: 4.00e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 4504401  131 LICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLpFVPSAEDV-YDCQVEHWGLDAPLLRHW 204
Cdd:cd21022  21 LRCWALGFYPAEIILTWQRDGEDQTQDVELVETRPAGDGTFQKWAAV-VVPSGEEQrYTCHVQHEGLPEPLMLRW 94
IgC1_SIRP_domain_2 cd05772
Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; member of the C1-set of Ig ...
113-206 4.30e-06

Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig)-like domain in Signal-Regulatory Protein (SIRP), domain 2 (C1 repeat 1). The SIRPs belong to the "paired receptors" class of membrane proteins that comprise several genes coding for proteins with similar extracellular regions, but very different transmembrane/cytoplasmic regions with different (activating or inhibitory) signaling potentials. They are commonly on NK cells, but are also on many myeloid cells. Their extracellular region contains three Immunoglobulin superfamily domains, a single V-set and two C1-set IgSF domains. Their cytoplasmic tails contain either ITIMs or transmembrane regions that have positively charged residues that allow an association with adaptor proteins, such as DAP12/KARAP, containing ITAMs. There are 3 distinct SIRP members: alpha, beta, and gamma. SIRP alpha (also known as CD172a or SRC homology 2 domain-containing protein tyrosine phosphatase substrate 1/Shps-1) is a membrane receptor that interacts with a ligand CD47 expressed on many cells and gives an inhibitory signal through immunoreceptor tyrosine-based inhibition motifs in the cytoplasmic region that interact with phosphatases SHP-1 and SHP-2. SIRP beta has a short cytoplasmic region and associates with a transmembrane adapter protein DAP12 containing immunoreceptor tyrosine-based activation motifs to give an activating signal. SIRP gamma contains a very short cytoplasmic region lacking obvious signaling motifs, but also binds CD47, but with much less affinity.


Pssm-ID: 409429  Cd Length: 102  Bit Score: 44.24  E-value: 4.30e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  113 PRVTVlPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEgvAQTSFYSQPD-HLFRKFHYLPFVPSAEDVYD--- 188
Cdd:cd05772   5 PLVSG-PSGRATPGQTVSFTCKSHGFSPRDITLKWFKNGNELSA--LQTTVFPEGDsVSYSVSSTVQVVLTKDDVHSqlt 81
                        90
                ....*....|....*...
gi 4504401  189 CQVEHWGLDAPLLRHWEL 206
Cdd:cd05772  82 CEVAHVTLQAPLRGTANL 99
IgC1_MHC_Ib_HLA-H cd21021
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
111-204 9.99e-06

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen H; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen H (HLA-H). HLA-H (also known as hereditary hemochromatosis protein; HFE) is a major histocompatibility complex (MHC) class I-like protein that is mutated in Hereditary Hemochromatosis. HFE is a protein of 343 amino acids that includes a signal peptide, an extracellular transferrin receptor-binding region (a1 and a2), an immunoglobulin-like domain (a3), a transmembrane region, and a short cytoplasmic tail. HFE binds beta-2-microglobulin to form a heterodimer expressed at the cell surface. It binds transferrin receptor (TFRC) in its extracellular alpha1-alpha2 domain. HFE plays an important part in the regulation of hepcidin expression in response to iron overload and the liver is important in the pathophysiology of HFE-associated hemochromatosis. Nine HFE splicing variants have been reported with transcripts lacking exon 2 or exon 3, or exons 2-3, 2-4, or 2-5. Diverse mutations involving HFE introns and exons discovered in persons with hemochromatosis or their family members cause or probably cause high iron phenotypes. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409612  Cd Length: 94  Bit Score: 43.23  E-value: 9.99e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  111 VPPRVTVLPKSRVELgqpNILICIVDNIFPPVINITWLRNGQTV-TEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDC 189
Cdd:cd21021   3 VPPLVKVTHHVTSSV---TTLRCRALNYYPQNITMKWLKDKQPMdAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQRYTC 79
                        90
                ....*....|....*
gi 4504401  190 QVEHWGLDAPLLRHW 204
Cdd:cd21021  80 QVEHPGLDQPLIVIW 94
IgC1_MHC_Ia_H-2Dd cd21020
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H2-Dd; member of the ...
112-204 1.69e-05

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H2-Dd; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H2-Dd. Mouse MHC is composed of 11 subclasses. It includes the classical MHC class I (MHC-Ia) that comprises H-2D, H-2K and H-2L subclasses, the non-classical MHC class I (MHCIb) that comprises H-2Q, H-2M and H-2T subclasses, the classical MHC class II (MHC-IIa) that includes H-2A(I-A) and H-2E(I-E) subclasses, and the non-classical MHC class II (MHC-IIb) comprises H-2M and H-2O. H-2K, H-2D, and H-2L are 80 to 90% homologous at the amino acid level yet appear to be involved in different recognition reactions and are differentially expressed on lymphoid cells. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409611  Cd Length: 95  Bit Score: 42.44  E-value: 1.69e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  112 PPRVTVLPKSRVElgQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQV 191
Cdd:cd21020   5 PPKAHVTHHRRPE--GDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGTFQKWASVVVPLGKEQKYTCHV 82
                        90
                ....*....|...
gi 4504401  192 EHWGLDAPLLRHW 204
Cdd:cd21020  83 EHEGLPEPLTLRW 95
IgC1_MHC_Ib_T10_T22_like cd21016
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of T10, T22, and similar ...
112-205 1.95e-05

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of T10, T22, and similar proteins; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of the murine H-2T-encoded T10, T22, and similar proteins. T10 and T22 are highly related nonclassical major histocompatibility complex (MHC) class Ib proteins that bind to certain gammadelta T cell receptors (TCRs) in the absence of other components. Classical MHC class I (class Ia) molecules participate in immune responses by presenting peptide antigens to cytolytic alpha beta T cells. Many nonclassical MHC class I (class Ib) molecules have distinct antigen-binding capabilities, suggesting that they have evolved for specific tasks that are distinct from those of MHC class Ia. Members of the IgC family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, and the IgC domain is involved in oligomerization and molecular interactions.


Pssm-ID: 409607  Cd Length: 97  Bit Score: 42.39  E-value: 1.95e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  112 PPRVTVLPKSRVElgQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQV 191
Cdd:cd21016   5 PPKAHVTRHPRPE--GDVTLRCWALGFYPADITLTWQKDGEELTQDMEFVETRPAGDGTFQKWAAVVVPLGKEQSYTCHV 82
                        90
                ....*....|....
gi 4504401  192 EHWGLDAPLLRHWE 205
Cdd:cd21016  83 YHEGLPEPLTLRWE 96
IgC1_MHC_Ia_H2Db_H2Ld cd21018
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
115-204 2.10e-05

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) H2Db and H2Ld; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) H2Db and H2Ld. H-2Ld complexed with peptide QL9 (or p2Ca) and complexed with influenza virus peptide NP366-374 (ASNEN-METM), respectively are high-affinity alloantigens for the 2C T cell receptor (TCR). The a1-a2 super domains of H-2Ld, H-2Db, and H-2Kb closely superimpose. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409609  Cd Length: 95  Bit Score: 42.42  E-value: 2.10e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  115 VTVLPKSRVELgqpnILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHW 194
Cdd:cd21018  10 VTHHPRSKGEV----TLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTCRVYHE 85
                        90
                ....*....|
gi 4504401  195 GLDAPLLRHW 204
Cdd:cd21018  86 GLPEPLTLRW 95
IgC1_MHC_Ia_HLA-A cd21027
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
131-204 7.66e-05

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) A; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) A. The classical class I molecules (HLA-A, -B, and -C) are responsible for the presentation of endogenous antigen to CD8+ T cells. The receptor is a heterodimer, and is composed of a heavy alpha chain and smaller beta chain. The alpha chain is encoded by a variant HLA-A gene, and the beta chain (beta-2-microglobulin) is an invariant beta-2-microglobulin molecule. The beta-2-microglobulin protein is coded for by a separate region of the human genome. HLA-A2 is associated with spontaneous abortions, HIV, and Hodgkin lymphoma. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409618  Cd Length: 95  Bit Score: 40.59  E-value: 7.66e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 4504401  131 LICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLpFVPSA-EDVYDCQVEHWGLDAPLLRHW 204
Cdd:cd21027  22 LRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAV-VVPSGqEQRYTCHVQHEGLPKPLTLRW 95
IgC1_MHC_Ib_HLA-Cw3-4 cd21025
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of HLA-Cw3 and HLA-Cw4; ...
131-205 9.34e-05

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of HLA-Cw3 and HLA-Cw4; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of HLA-Cw3 and HLA-Cw4. HLA-C belongs to the MHC class I heavy chain receptors. The C receptor is a heterodimer consisting of a HLA-C mature gene product and beta-2-microglobulin. The mature C chain is anchored in the membrane. MHC Class I molecules, like HLA-C, are expressed in nearly all cells, and present small peptides to the immune system which surveys for non-self peptides. HLA-C is a locus on chromosome 6, which encodes for a large number of HLA-C alleles that are Class-I MHC receptors. Class Ib histocompatibility leukocyte antigens (HLA)-Cw3 and (HLA)-Cw4 are ligands for the natural killer (NK) cell inhibitory receptors KIR2DL2 and KIR2DL1, respectively. HLA-Cw3 and related alleles (HLA-Cw1, -Cw7, and -Cw8) contain Ser77 and Asn80 and interact with KIR that are reactive with the GL183 antibody Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. HLA-Cw4 and related alleles (HLA-Cw2, -Cw5, and -Cw6) have Asn77 and Lys80 and are recognized by KIR reactive with the EB6 15 or HP-3E4 16 antibody. Members of the IgC family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, and the IgC domain is involved in oligomerization and molecular interactions.


Pssm-ID: 409616  Cd Length: 96  Bit Score: 40.56  E-value: 9.34e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 4504401  131 LICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLpFVPSAEDV-YDCQVEHWGLDAPLLRHWE 205
Cdd:cd21025  22 LRCWALGFYPAEITLTWQWDGEDQTQDTELVETRPAGDGTFQKWAAV-VVPSGEEQrYTCHVQHEGLPEPLTLRWE 96
IgC1_MHC_Ib_Qa-2 cd21014
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-2; member of the ...
112-204 9.43e-05

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-2; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of QA-2. Qa-2 is a nonclassical MHC Ib antigen, which has been implicated in both innate and adaptive immune responses, as well as embryonic development. Qa-2 has an unusual peptide binding specificity in that it requires two dominant C-terminal anchor residues and is capable of associating with a substantially more diverse array of peptide sequences than other nonclassical MHC. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409605  Cd Length: 94  Bit Score: 40.50  E-value: 9.43e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  112 PPR--VTVLPKSRVELgqpnILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDC 189
Cdd:cd21014   4 PPKahVTHHPRSYGAV----TLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTC 79
                        90
                ....*....|....*
gi 4504401  190 QVEHWGLDAPLLRHW 204
Cdd:cd21014  80 HVNHEGLPEPLTLRW 94
IgC1_MHC-like_ZAG cd21010
Immunoglobulin domain of Zn-alpha2-glycoprotein (ZAG); member of the C1-set of Ig superfamily ...
112-204 1.15e-04

Immunoglobulin domain of Zn-alpha2-glycoprotein (ZAG); member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin domain of Zn-alpha2-glycoprotein (ZAG). ZAG is a soluble protein that is present in serum and other body fluids. ZAG stimulates lipid degradation in adipocytes and causes the extensive fat losses associated with some advanced cancers. The 2.8 angstrom crystal structure of ZAG resembles a class I major histocompatibility complex (MHC) heavy chain, but ZAG does not bind the class I light chain beta-2-microglobulin. The ZAG structure includes a large groove analogous to class I MHC peptide binding grooves. Instead of a peptide, the ZAG groove contains a nonpeptidic compound that may be implicated in lipid catabolism under normal or pathological conditions. IgC_MHC_I_alpha3; Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I alpha chain. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409601  Cd Length: 93  Bit Score: 40.00  E-value: 1.15e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  112 PPRVTVlpKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHlfrkfhYLPFV-----PSAEDV 186
Cdd:cd21010   4 PPSVSV--TSHVAPGKNRTLKCLAYDFYPRGISLHWTRAGKVQESESGGDVLPSGNGT------YQSWVvvevpPQDRAP 75
                        90
                ....*....|....*...
gi 4504401  187 YDCQVEHWGLDAPLLRHW 204
Cdd:cd21010  76 YSCHVEHSSLAQPLTVPW 93
IgC1_MHC_Ib_HLA-E cd21024
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
131-204 1.62e-04

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) E; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) E. HLA-E is the first human class Ib major histocompatibility complex molecule to be crystallized. Like other MHC class I molecules, HLA-E is a heterodimer consisting of an a heavy chain and light chain beta-2-microglobulin. HLA-E is highly conserved and almost nonpolymorphic, and has recently been shown to be the first specialized ligand for natural killer cell receptors. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409615  Cd Length: 95  Bit Score: 39.77  E-value: 1.62e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 4504401  131 LICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLpFVPSAED-VYDCQVEHWGLDAPLLRHW 204
Cdd:cd21024  22 LRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDGTFQKWAAV-VVPSGEEqRYTCHVQHEGLPEPVTLRW 95
IgC1_MHC_Ia_H-2Kb cd21019
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H-2Kb; member of the ...
113-204 2.48e-04

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H-2Kb; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H-2Kb. H-2Kb is an alloantigen for the 2C T cell receptor (TCR). H-2Kb forms a complex with beta-2-microglobulin, and a peptide, including VSV-8 (RGYVYNGL), SEV-9 (FAPGNYPAL), and OVA-8 (SIINFEKL). Comparison of the OVA-8, VSV-8, and SEV-9 complexes with H-2Kb indicates that four side chains (Lys-66, Glu-152, Arg-155, and Trp-167) adopt peptide-specific conformations. H-2Kb paralogs include H-2Db, H-2Kbml and H-2KbI1s. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409610  Cd Length: 94  Bit Score: 39.32  E-value: 2.48e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  113 PRVTVLPKSRVElgQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVE 192
Cdd:cd21019   5 PKAHVTHHSRPE--DKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGTFQKWASVVVPLGKEQYYTCHVY 82
                        90
                ....*....|..
gi 4504401  193 HWGLDAPLLRHW 204
Cdd:cd21019  83 HQGLPEPLTLRW 94
IgC1_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member ...
112-193 4.64e-04

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin constant domain (IgC) of mu heavy chains. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


Pssm-ID: 409513  Cd Length: 99  Bit Score: 38.53  E-value: 4.64e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  112 PPRVTVLPKSRVEL--GQPNILICIVDNIFPPVINITWLRNGQTVTEGvaqTSFYSQP-----DHLFRKFHYLPFVPSA- 183
Cdd:cd16093   1 PPTVSLHAPSREEFlgNRTATFVCLATGFSPKTISFKWLRNGKEVTSS---TGAVVEEpkedgKTLYSATSFLTITESEw 77
                        90
                ....*....|..
gi 4504401  184 --EDVYDCQVEH 193
Cdd:cd16093  78 ksQTEFTCEFKH 89
IgC1_CH2_IgE cd05847
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of ...
113-198 4.68e-04

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second constant domain of the heavy chain of immunoglobulin E (IgE). The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta, and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). The different classes of antibodies vary in their heavy chains; the IgE class has the epsilon type. This domain (Cepsilon2) of IgE is in place of the flexible hinge region found in IgG.


Pssm-ID: 409434  Cd Length: 97  Bit Score: 38.55  E-value: 4.68e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  113 PRVTVLPKSRVELGQPNI--LICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFR--------KFHYLpfvps 182
Cdd:cd05847   1 PTVQILHSSCASTLTSETiqLLCLISGYTPSTIEVEWLVDGQVATLSAASTAPQKEEGGTFSttsklnvtQEDWK----- 75
                        90
                ....*....|....*.
gi 4504401  183 AEDVYDCQVEHWGLDA 198
Cdd:cd05847  76 SGKTYTCKVTHQGTTF 91
IgC1_MHC_H-2_TLA cd21012
H-2 class I histocompatibility complex TLA (thymus leukemia antigen); member of the C1-set of ...
112-204 5.01e-04

H-2 class I histocompatibility complex TLA (thymus leukemia antigen); member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the major histocompatibility complex (MHC) H-2 class I histocompatibility complex TLA (thymus leukemia antigen). The murine MHC class I histocompatibility TLA (Thymus leukemia antigen), which is encoded in the T region by T3 and T18 genes, is expressed mainly by intestinal epithelial cells and thymocytes. The murine TLAs are class I, beta-2-microglobulin-associated glycoproteins. The TLA function is not defined by antigen presentation, but rather by its relatively high affinity binding to CD8-alpha-alpha compared with CD8-alpha-beta. The existence of a human homolog for murine TLA remains unresolved. This group is a member of the C1-set Ig domains, which have one beta sheet that is formed by strands A, B, E, and D and the other strands by G, F, C, and C'.


Pssm-ID: 409603  Cd Length: 95  Bit Score: 38.17  E-value: 5.01e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  112 PPRVTVLPKSRVElgQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQV 191
Cdd:cd21012   5 PPKTHVTHHPRPE--GYVTLRCWALGFYPAHITLTWQLNGEELIQDTELVETRPAGDGTFQKWAAVVVPSGEEQKYTCHV 82
                        90
                ....*....|...
gi 4504401  192 EHWGLDAPLLRHW 204
Cdd:cd21012  83 YHEGLPEPLTLRW 95
C2-set_2 pfam08205
CD80-like C2-set immunoglobulin domain; These domains belong to the immunoglobulin superfamily.
117-199 7.50e-04

CD80-like C2-set immunoglobulin domain; These domains belong to the immunoglobulin superfamily.


Pssm-ID: 400489  Cd Length: 89  Bit Score: 37.78  E-value: 7.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401    117 VLPKSRVELGQPN-ILICIVDNIFPPViNITWLRNGQTVTEGVAQTSFYSQPdhlfrKFHY----LPFVPSAED---VYD 188
Cdd:pfam08205   4 EPPASLLEGEGPEvVATCSSAGGKPAP-RITWYLDGKPLEAAETSSEQDPES-----GLVTvtseLKLVPSRSDhgqSLT 77
                          90
                  ....*....|.
gi 4504401    189 CQVEHWGLDAP 199
Cdd:pfam08205  78 CQVSYGALRGS 88
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
112-166 2.67e-03

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 36.00  E-value: 2.67e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 4504401    112 PPRVTVLPKS-RVELGQPNILICIVDNIFPPviNITWLRNGQTVTEGVAQTSFYSQ 166
Cdd:pfam13927   1 KPVITVSPSSvTVREGETVTLTCEATGSPPP--TITWYKNGEPISSGSTRSRSLSG 54
IgC1_SIRP_domain_3 cd16085
Signal-regulatory protein (SIRP) immunoglobulin-like domain 3; member of the C1-set of Ig ...
111-193 2.89e-03

Signal-regulatory protein (SIRP) immunoglobulin-like domain 3; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig)-like domain in Signal-Regulatory Protein (SIRP), domain 3 (C1 repeat 2). The SIRPs belong to the "paired receptors" class of membrane proteins that comprise several genes coding for proteins with similar extracellular regions but very different transmembrane/cytoplasmic regions with different (activating or inhibitory) signaling potentials. They are commonly on NK cells, but are also on many myeloid cells. Their extracellular region contains three Immunoglobulin superfamily domains a single V-set and two C1-set IgSF domains. Their cytoplasmic tails that contain either ITIMs or transmembrane regions that have positively charged residues that allow an association with adaptor proteins, such as DAP12/KARAP, containing ITAMs. There are 3 distinct SIRP members: alpha, beta, and gamma. SIRP alpha (also known as CD172a or SRC homology 2 domain-containing protein tyrosine phosphatase substrate 1/Shps-1) is a membrane receptor that interacts with a ligand CD47 expressed on many cells and gives an inhibitory signal through immunoreceptor tyrosine-based inhibition motifs in the cytoplasmic region that interact with phosphatases SHP-1 and SHP-2. SIRP beta has a short cytoplasmic region and associates with a transmembrane adapter protein DAP12 containing immunoreceptor tyrosine-based activation motifs to give an activating signal. SIRP gamma contains a very short cytoplasmic region lacking obvious signaling motifs but also binds CD47, but with much less affinity.


Pssm-ID: 409507  Cd Length: 96  Bit Score: 36.25  E-value: 2.89e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504401  111 VPPRVTVLPKSRVELGQPNIlICIVDNIFPPVINITWLRNGQTVTEGVAQTsFYSQPDHLFRKFHYLPFVPSA--ED-VY 187
Cdd:cd16085   1 VPPTLEVTQQPTMVWNQVNV-TCQVEKFYPQRLQLTWLENGNVSRTETPST-LTVNKDGTYNWTSWLLVNVSAhrEDvVL 78

                ....*.
gi 4504401  188 DCQVEH 193
Cdd:cd16085  79 TCQVEH 84
IgC1_MHC-like_FcRn cd21011
immunoglobulin domain of neonatal Fc receptor, major histocompatibility complex (MHC)-like; ...
130-201 6.90e-03

immunoglobulin domain of neonatal Fc receptor, major histocompatibility complex (MHC)-like; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin domain of neonatal Fc receptor (FcRn). FcRn performs two distinct functions: the transport of maternal immunoglobulin G (IgG) to pre- or neonatal mammals which provides passive immunity and protection of IgG from normal serum protein catabolism. FcRn is related to class I MHC proteins, but lacks a functional peptide binding groove. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409602  Cd Length: 93  Bit Score: 35.09  E-value: 6.90e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 4504401  130 ILICIVDNIFPPVINITWLRNGQTVteGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLL 201
Cdd:cd21011  21 VLTCSAFSFYPPELQLRFLRNGLAA--GSGEGDFGPNGDGSFHAWSSLTVKSGDEHHYRCVVQHAGLAQPLT 90
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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