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Conserved domains on  [gi|6729998|pdb|1BX2|B]
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Chain B, Crystal Structure Of Hla-Dr2 (Dra0101,Drb11501) Complexed With A Peptide From Human Myelin Basic Protein

Protein Classification

MHC_II_beta and Ig domain-containing protein (domain architecture ID 10469867)

MHC_II_beta and Ig domain-containing protein

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
MHC_II_beta pfam00969
Class II histocompatibility antigen, beta domain;
12-85 4.19e-47

Class II histocompatibility antigen, beta domain;


:

Pssm-ID: 334331  Cd Length: 75  Bit Score: 148.59  E-value: 4.19e-47
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
1BX2_B         12 ECHFFNGTERVRFLDRYFYNQEESVRFDSDVGEFRAVTELGRPDAEYWNSQKDILEQARAAVDTYCRHNYGVVE 85
Cdd:pfam00969   2 ECYFTNGTERVRFLYRYIFNKEELARFDSDVGEFVAVTELGRPDAEYWNSQKDLLERLRAGVDTVCRHNYPFWE 75
Ig super family cl11960
Immunoglobulin domain; Immunoglobulin (Ig) domain found in the Ig superfamily. The Ig ...
95-188 2.06e-46

Immunoglobulin domain; Immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond.


The actual alignment was detected with superfamily member cd05766:

Pssm-ID: 353325  Cd Length: 94  Bit Score: 147.55  E-value: 2.06e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1BX2_B       95 PKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVE 174
Cdd:cd05766   1 PSVKISPSQTGSLSHPHLLVCHVWGFYPPEITVKWFKNGQEETEGVVSTELIPNGDWTYQILVMLETTPSRGDTYTCVVE 80
                        90
                ....*....|....
1BX2_B      175 HPSVTSPLTVEWRA 188
Cdd:cd05766  81 HSSLQEPLTVDWRP 94
 
Name Accession Description Interval E-value
MHC_II_beta pfam00969
Class II histocompatibility antigen, beta domain;
12-85 4.19e-47

Class II histocompatibility antigen, beta domain;


Pssm-ID: 334331  Cd Length: 75  Bit Score: 148.59  E-value: 4.19e-47
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
1BX2_B         12 ECHFFNGTERVRFLDRYFYNQEESVRFDSDVGEFRAVTELGRPDAEYWNSQKDILEQARAAVDTYCRHNYGVVE 85
Cdd:pfam00969   2 ECYFTNGTERVRFLYRYIFNKEELARFDSDVGEFVAVTELGRPDAEYWNSQKDLLERLRAGVDTVCRHNYPFWE 75
IgC_MHC_II_beta cd05766
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; ...
95-188 2.06e-46

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; IgC_MHC_II_beta: 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. In both humans and in mice these molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), for example on B-lymphocytes, monocytes, and macrophages. 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 protelytic 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: 143243  Cd Length: 94  Bit Score: 147.55  E-value: 2.06e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1BX2_B       95 PKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVE 174
Cdd:cd05766   1 PSVKISPSQTGSLSHPHLLVCHVWGFYPPEITVKWFKNGQEETEGVVSTELIPNGDWTYQILVMLETTPSRGDTYTCVVE 80
                        90
                ....*....|....
1BX2_B      175 HPSVTSPLTVEWRA 188
Cdd:cd05766  81 HSSLQEPLTVDWRP 94
MHC_II_beta smart00921
Class II histocompatibility antigen, beta domain; Class II MHC glycoproteins are expressed on ...
12-82 3.73e-45

Class II histocompatibility antigen, beta 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: 197989  Cd Length: 72  Bit Score: 143.51  E-value: 3.73e-45
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
1BX2_B          12 ECHFFNGTERVRFLDRYFYNQEESVRFDSDVGEFRAVTELGRPDAEYWNSQKDILEQARAAVDTYCRHNYG 82
Cdd:smart00921   2 ECYFSNGTEDVRYVVRYIYNKEELVRFDSDVGKFVAFTELGRPAAEYWNSQKDLLERLRAEVDTVCRHNYQ 72
C1-set pfam07654
Immunoglobulin C1-set domain;
97-177 4.31e-34

Immunoglobulin C1-set domain;


Pssm-ID: 336758  Cd Length: 85  Bit Score: 115.81  E-value: 4.31e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1BX2_B         97 VTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQTLVMLETVP---RSGEVYTCQV 173
Cdd:pfam07654   1 VYVFPPSPEELGKPNTLTCLVTGFYPPDITVTWLKNGQEVTEGVTTTPPSPNSDWTYQLSSYLTVTPsdwESGDTYTCRV 80

                  ....
1BX2_B        174 EHPS 177
Cdd:pfam07654  81 EHEG 84
IGc1 smart00407
Immunoglobulin C-Type;
110-181 1.28e-22

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 86.21  E-value: 1.28e-22
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
1BX2_B         110 HNLLVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQ---TLVMLETVPRSGEVYTCQVEHPSVTSP 181
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEVTEGVSTTDPLKNSDGTYFlssYLTVPASTWESGDVYTCQVTHEGLKEP 75
 
Name Accession Description Interval E-value
MHC_II_beta pfam00969
Class II histocompatibility antigen, beta domain;
12-85 4.19e-47

Class II histocompatibility antigen, beta domain;


Pssm-ID: 334331  Cd Length: 75  Bit Score: 148.59  E-value: 4.19e-47
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
1BX2_B         12 ECHFFNGTERVRFLDRYFYNQEESVRFDSDVGEFRAVTELGRPDAEYWNSQKDILEQARAAVDTYCRHNYGVVE 85
Cdd:pfam00969   2 ECYFTNGTERVRFLYRYIFNKEELARFDSDVGEFVAVTELGRPDAEYWNSQKDLLERLRAGVDTVCRHNYPFWE 75
IgC_MHC_II_beta cd05766
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; ...
95-188 2.06e-46

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; IgC_MHC_II_beta: 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. In both humans and in mice these molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), for example on B-lymphocytes, monocytes, and macrophages. 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 protelytic 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: 143243  Cd Length: 94  Bit Score: 147.55  E-value: 2.06e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1BX2_B       95 PKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVE 174
Cdd:cd05766   1 PSVKISPSQTGSLSHPHLLVCHVWGFYPPEITVKWFKNGQEETEGVVSTELIPNGDWTYQILVMLETTPSRGDTYTCVVE 80
                        90
                ....*....|....
1BX2_B      175 HPSVTSPLTVEWRA 188
Cdd:cd05766  81 HSSLQEPLTVDWRP 94
MHC_II_beta smart00921
Class II histocompatibility antigen, beta domain; Class II MHC glycoproteins are expressed on ...
12-82 3.73e-45

Class II histocompatibility antigen, beta 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: 197989  Cd Length: 72  Bit Score: 143.51  E-value: 3.73e-45
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
1BX2_B          12 ECHFFNGTERVRFLDRYFYNQEESVRFDSDVGEFRAVTELGRPDAEYWNSQKDILEQARAAVDTYCRHNYG 82
Cdd:smart00921   2 ECYFSNGTEDVRYVVRYIYNKEELVRFDSDVGKFVAFTELGRPAAEYWNSQKDLLERLRAEVDTVCRHNYQ 72
C1-set pfam07654
Immunoglobulin C1-set domain;
97-177 4.31e-34

Immunoglobulin C1-set domain;


Pssm-ID: 336758  Cd Length: 85  Bit Score: 115.81  E-value: 4.31e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1BX2_B         97 VTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQTLVMLETVP---RSGEVYTCQV 173
Cdd:pfam07654   1 VYVFPPSPEELGKPNTLTCLVTGFYPPDITVTWLKNGQEVTEGVTTTPPSPNSDWTYQLSSYLTVTPsdwESGDTYTCRV 80

                  ....
1BX2_B        174 EHPS 177
Cdd:pfam07654  81 EHEG 84
IGc1 smart00407
Immunoglobulin C-Type;
110-181 1.28e-22

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 86.21  E-value: 1.28e-22
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
1BX2_B         110 HNLLVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQ---TLVMLETVPRSGEVYTCQVEHPSVTSP 181
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEVTEGVSTTDPLKNSDGTYFlssYLTVPASTWESGDVYTCQVTHEGLKEP 75
IgC cd00098
Immunoglobulin Constant (IgC) domain; Members of the IgC family are components of ...
97-187 2.18e-21

Immunoglobulin Constant (IgC) domain; 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: 319274  Cd Length: 95  Bit Score: 83.64  E-value: 2.18e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1BX2_B       97 VTVYPSKTQP-LQHHNLLVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQTLVMLETVP---RSGEVYTCQ 172
Cdd:cd00098   1 VTLLPPSPEEkLGGTVTLVCLVSGFYPKDITVTWLKNGKEVTSGVSTTPPTKNSDGTFSVTSYLTVPPsdwDEGTTYTCE 80
                        90
                ....*....|....*
1BX2_B      173 VEHPSVTSPLTVEWR 187
Cdd:cd00098  81 VSHESLSQPVSKSLN 95
IgC_MHC_I_alpha3 cd07698
Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain; ...
93-186 2.60e-20

Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain; 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 beta2 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: 143322  Cd Length: 93  Bit Score: 80.79  E-value: 2.60e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1BX2_B       93 VQPKVTVYPSktQPLQHHNLLVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQ 172
Cdd:cd07698   1 VPPEVRVTRK--RAPDGSLTLSCHATGFYPRDIEVTWLRDGEDSVDDVESGEILPNGDGTYQLWVTLEVPPEDKARYSCR 78
                        90
                ....*....|....
1BX2_B      173 VEHPSVTSPLTVEW 186
Cdd:cd07698  79 VEHSGLKEPLIVPW 92
IgC_beta2m cd05770
Class I major histocompatibility complex (MHC) beta2-microglobulin; IgC_beta2m: ...
95-187 9.26e-19

Class I major histocompatibility complex (MHC) beta2-microglobulin; IgC_beta2m: Immunoglobulin-like domain in beta2-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 then excreted.


Pssm-ID: 143247  Cd Length: 93  Bit Score: 76.75  E-value: 9.26e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1BX2_B       95 PKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFLNGQE-EKAGMvsTGLIQNGDWTFQTLVMLETVPRSGEVYTCQV 173
Cdd:cd05770   2 PKVQVYSRFPAENGKPNVLNCYVTGFHPPDIEIRLLKNGVKiPKVEQ--SDLSFSKDWTFYLLKSTEFTPTKGDEYACRV 79
                        90
                ....*....|....
1BX2_B      174 EHPSVTSPLTVEWR 187
Cdd:cd05770  80 RHNSMSEPKKYKWD 93
IgC_MHC_II_alpha cd05767
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; ...
95-186 3.89e-15

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; IgC_MHC_II_alpha: Immunoglobulin (Ig) domain of 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. In both humans and in mice these molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), for example on B-lymphocytes, monocytes, and macrophages. 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 protelytic 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: 143244  Cd Length: 94  Bit Score: 67.37  E-value: 3.89e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1BX2_B       95 PKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVE 174
Cdd:cd05767   2 PEVTVFSLKPVELGEPNTLICFVDNFFPPVLNVTWLKNGVPVTDGVSETRYYPRQDLSFQKFSYLNFTPEEGDIYSCIVE 81
                        90
                ....*....|..
1BX2_B      175 HPSVTSPLTVEW 186
Cdd:cd05767  82 HWGLETPATRYW 93
IgC_L cd07699
Immunoglobulin Constant domain; IgC_L: Immunoglobulin (Ig) light chain constant (C) domain. ...
95-183 7.02e-14

Immunoglobulin Constant domain; IgC_L: 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: 319325  Cd Length: 99  Bit Score: 64.01  E-value: 7.02e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1BX2_B       95 PKVTVYPSKTQPLQHHNL-LVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQ---TLVMLETVPRSGEVYT 170
Cdd:cd07699   2 PSVTIFPPSSEELSSGKAtLVCLINKFYPGFATVTWKVDGSTVSSGVTTSKTEQQSDNTYSmssYLTLSSSDWNKHKVYT 81
                        90
                ....*....|...
1BX2_B      171 CQVEHPSVTSPLT 183
Cdd:cd07699  82 CEVTHEGLSSTIT 94
IgC_CH2_IgE cd05847
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); ...
113-179 1.35e-11

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); IgC_CH2_IgE: 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 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) and three (in alpha, delta, and gamma) or four (in 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: 143255  Cd Length: 94  Bit Score: 58.19  E-value: 1.35e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1BX2_B      113 LVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQT---LVMLETVPRSGEVYTCQVEHPSVT 179
Cdd:cd05847  19 LLCLISGYTPGTIEVEWLVDGQVATLVAASTAPQKEEGSTFSTtseLNVTQEDWKSGKTYTCKVTHQGTT 88
IgC_Tapasin_R cd05771
Tapasin-R immunoglobulin-like domain; IgC_Tapasin_R: Immunoglobulin-like domain on Tapasin-R. ...
94-184 3.56e-09

Tapasin-R immunoglobulin-like domain; IgC_Tapasin_R: 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: 319313  Cd Length: 138  Bit Score: 52.52  E-value: 3.56e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1BX2_B       94 QPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFLNGQEEKAGMVS------TGLIQNGDWTFQ---TLVMLETVPR 164
Cdd:cd05771  38 PPRVRLSLEKTVSIEEPQTLICHIAGYYPLDVQVEWTREPPGDSPPRVSvsnvsfSSHRQHADGTYSlssALTLEPGTPH 117
                        90       100
                ....*....|....*....|
1BX2_B      165 SGEVYTCQVEHPSVTSPLTV 184
Cdd:cd05771 118 PGATYTCRVTHVALETPVSV 137
IgC_CH3_IgAGD_CH4_IgAEM cd05768
CH4 domain (fourth constant Ig domain of the heavy chain) in immunoglobulin; ...
95-184 5.92e-08

CH4 domain (fourth constant Ig domain of the heavy chain) in immunoglobulin; IgC_CH3_IgAGD_CH4_IgAEM: Contains 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 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) and three (in alpha, delta and gamma) or four (in 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: 319312  Cd Length: 100  Bit Score: 48.46  E-value: 5.92e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1BX2_B       95 PKVTVYPSKTQPLQHHNL-LVCSVSGFYPGSIEVRWFLNGQE-EKAGMVSTGLIQN-GDWTFQTLVMLeTVPRS----GE 167
Cdd:cd05768   1 PSVYLLPPPEEELSLNTVtLTCLVKGFSPEDIFVRWLQNGQPlPEEDYKTTTPVKEeSDGSFFVYSKL-TVTASdwksGD 79
                        90
                ....*....|....*..
1BX2_B      168 VYTCQVEHPSVTSPLTV 184
Cdd:cd05768  80 VFSCVVGHEALPLQFTQ 96
IgC_TCR_beta cd05769
T cell receptor (TCR) beta chain constant immunoglobulin domain; IgC_TCR_beta: Constant domain ...
94-143 1.80e-07

T cell receptor (TCR) beta chain constant immunoglobulin domain; IgC_TCR_beta: Constant domain of the beta chain of alpha/beta T-cell antigen receptors (TCRs). 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: 143246  Cd Length: 115  Bit Score: 47.37  E-value: 1.80e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
1BX2_B       94 QPKVTVYPSKTQPLQHHN--LLVCSVSGFYPGSIEVRWFLNGQEEKAGmVST 143
Cdd:cd05769   2 PPTVAIFPPSEAEIRNKRkaTLVCLATGFYPDHVSLSWKVNGKEVTDG-VAT 52
IgC_SIRP_domain_3 cd16085
Signal-regulatory protein (SIRP) immunoglobulin-like domain 3; Immunoglobulin (Ig)-like domain ...
105-191 1.07e-06

Signal-regulatory protein (SIRP) immunoglobulin-like domain 3; 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: 319334  Cd Length: 104  Bit Score: 45.10  E-value: 1.07e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1BX2_B      105 QPLQHHNL--LVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTgLIQNGDWTFQ-TLVMLETVP--RSGEVYTCQVEH---P 176
Cdd:cd16085  10 QPTMVWNQvnVTCQVQKFYPQKLQLTWLENGNVSRTEEPST-LTVNKDGTYNwTSWLLVNVSahREDVVLTCQVEHdgqP 88
                        90
                ....*....|....*
1BX2_B      177 SVTSPLTVEWRARSE 191
Cdd:cd16085  89 AVTKNHTLVVSAHQK 103
IgC_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin; IgC_CH2: The ...
113-179 1.40e-06

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin; IgC_CH2: 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 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) and three (in alpha, delta and gamma) or four (in 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: 319342  Cd Length: 100  Bit Score: 44.61  E-value: 1.40e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
1BX2_B      113 LVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTGL----IQNGDWTFQTLVML---ETVPRSGEVYTCQVEHPSVT 179
Cdd:cd16093  21 LICQATGFSPRQISVSWLREGKQVGSGVTTDAVeaeaKESGPTTFRVTSTLtitESEWLSQSMFTCRVDHRGLT 94
IgC_SIRP_domain_2 cd05772
Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; IgC: immunoglobulin (Ig)-like ...
94-183 5.30e-06

Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; IgC: 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 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: 319314  Cd Length: 103  Bit Score: 43.07  E-value: 5.30e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1BX2_B       94 QPKVTVYPSKTQPLQHHNLlVCSVSGFYPGSIEVRWFLNGQEEKAGMvSTGLIQNGDWTFQTLVMLETVPRSGEV---YT 170
Cdd:cd05772   4 LPVVSGPAARATPGQTVSF-TCKSHGFSPRDITLKWFKNGNELSALQ-TTVLPEGDSVSYSVSSTVQVVLTKDDVhsqLT 81
                        90
                ....*....|...
1BX2_B      171 CQVEHPSVTSPLT 183
Cdd:cd05772  82 CEVAHVTLQAPLR 94
Ig2_Necl-3 cd05884
Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell ...
113-180 2.54e-04

Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2)); Ig2_Necl-3: second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2)). Nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 - Necl-5). These have an extracellular region containing three Ig-like domains, one transmembrane region, and one cytoplasmic region. Necl-3 has been shown to accumulate in tissues of the central and peripheral nervous system, where it is expressed in ependymal cells and myelinated axons. It is observed at the interface between the axon shaft and the myelin sheath. Ig domains are likely to participate in ligand binding and recognition.


Pssm-ID: 319320  Cd Length: 83  Bit Score: 38.06  E-value: 2.54e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
1BX2_B      113 LVCSVSGFYPGSiEVRWFLNGQEEKAGMVSTGLIQNGDwTF---QTLVMLETVPRSGEVYTCQVEHPSVTS 180
Cdd:cd05884   4 LTCKTSGSKPAA-DIRWFKNDKEIKDVKYLKEEDANRK-TFtvsSTLDFRVDRSDDGVAIICRVDHESLNA 72
IgC_TCR_gamma cd07697
T cell receptor (TCR) gamma chain constant immunoglobulin domain; IgC_TCR_gamma; ...
95-175 5.15e-04

T cell receptor (TCR) gamma chain constant immunoglobulin domain; IgC_TCR_gamma; immunoglobulin (Ig) constant (C) domain of the gamma chain of gamma-delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha-beta TCRs but a small subset contain gamma-delta TCRs. Alpha-beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma-delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing, and MHC independently of the bound peptide. Gamma-delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds.


Pssm-ID: 319324  Cd Length: 97  Bit Score: 37.58  E-value: 5.15e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1BX2_B       95 PKVTVYP--SKTQPLQHHNLLVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQTLVMLeTVPRS--GEVYT 170
Cdd:cd07697   1 PKPTIFPpsTAELEKQSKGFYLCLLEDFFPDVIEVHWKEDGKEQKELGSQDSVTKKGNNTYSLISWL-TVTKLslGKPIR 79

                ....*
1BX2_B      171 CQVEH 175
Cdd:cd07697  80 CHYKH 84
Ig2_Necl-1-4_like cd05761
Second immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 - Necl-4 (also ...
113-180 7.06e-04

Second immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 - Necl-4 (also known as cell adhesion molecules CADM3, CADM1, CADM2, and CADM4, respectively); Ig2_Necl-1-4_like: domain similar to the second immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 (also known as cell adhesion molecule 3 (CADM3)), Necl-2 (CADM1), Necl-3 (CADM2) and Necl-4 (CADM4). These nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 - Necl-5). These have an extracellular region containing three Ig-like domains, one transmembrane region, and one cytoplasmic region. The N-terminal Ig-like domain of the extracellular region belongs to the V-type subfamily of Ig domains, is essential to cell-cell adhesion, and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-1 and Necl-2 have Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-1 is specifically expressed in neural tissue and is important to the formation of synapses, axon bundles, and myelinated axons. Necl-2 is expressed in a wide variety of tissues, and is a putative tumour suppressor gene, which is downregulated in aggressive neuroblastoma. Necl-3 has been shown to accumulate in tissues of the central and peripheral nervous system, where it is expressed in ependymal cells and myelinated axons. It is observed at the interface between the axon shaft and the myelin sheath. Necl-4 is expressed on Schwann cells, and plays a key part in initiating peripheral nervous system (PNS) myelination. Necl-4 participates in cell-cell adhesion and is proposed to play a role in tumor suppression.


Pssm-ID: 319311  Cd Length: 83  Bit Score: 36.77  E-value: 7.06e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
1BX2_B      113 LVCSVSGFYPGSiEVRWFLNGQEEKAGMVSTGLIQNGD-WTFQTLVMLEtVPR--SGEVYTCQVEHPSVTS 180
Cdd:cd05761   4 LTCTSSGSKPAA-TLRWYKDDQELKGVPDVSESDENGKtYTVTSSLTFQ-VDRkdDGAPIICQVDHPSLTS 72
IgC_CH1_IgAEGM cd04985
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin; IgC_CH2: The first ...
115-185 3.98e-03

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin; IgC_CH2: The first immunoglobulin constant domain of alpha, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding 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 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) and three (in alpha, delta and gamma) or four (in 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: 319288  Cd Length: 96  Bit Score: 34.96  E-value: 3.98e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
1BX2_B      115 CSVSGFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDwtFQTLVMLETVPRS----GEVYTCQVEHPSVTS-PLTVE 185
Cdd:cd04985  23 CLATGFFPEPVTFTWNSGSNSTSGVKTFPAVLQSGG--LYTASSQLTVPASewksKKSFYCKVEHPPTTSvDKEVP 96
Ig cd00096
Immunoglobulin domain; Immunoglobulin (Ig) domain found in the Ig superfamily. The Ig ...
113-185 7.50e-03

Immunoglobulin domain; Immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond.


Pssm-ID: 319273  Cd Length: 70  Bit Score: 33.75  E-value: 7.50e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
1BX2_B      113 LVCSVSGfYPgSIEVRWFLNGQEEKAGMVSTGLIQNGDWtfqTLVMLETVPRSGEVYTCQVEHPSVTSPLTVE 185
Cdd:cd00096   3 LTCSASG-NP-PPTITWLKNGKPLPSSSRFRRRSSGGNG---TLTISNVTPEDSGTYTCVASNSAGSASASVT 70
ig pfam00047
Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of ...
113-184 7.98e-03

Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions.


Pssm-ID: 333796  Cd Length: 86  Bit Score: 34.08  E-value: 7.98e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
1BX2_B        113 LVCSVSGFYPGsIEVRWFLNGQEEKAGMVsTGLIQNGDWTFQTLVMLETVPRSGEvYTCQVEHPSVTSPLTV 184
Cdd:pfam00047  16 LTCSASTGSPL-PDVTWSKEGGTLIESLR-VGHDNGRTTQSSLLISNVTLEDAGT-YTCVVNNPGGPATLST 84
IgC_CH1_IgD cd16092
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin; IgC_CH1: The first ...
100-180 8.04e-03

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin; IgC_CH1: The first immunoglobulin constant domain (IgC), of immunoglobulin (Ig) delta heavy chains. This domain is found on the Fab antigen-binding 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 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) and three (in alpha, delta and gamma) or four (in 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: 319341  Cd Length: 96  Bit Score: 34.43  E-value: 8.04e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1BX2_B      100 YPSKTQPLqhhnLLVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTglIQNGDWTFQTLVMLETvP----RSGEvYTCQVEH 175
Cdd:cd16092  13 HPKDNSPV----VLACLITGYHPTSVTVTWYMGTQSQPQRTFPE--IQRRDSYYMTSSQLST-PlqqwRQGE-YKCVVQH 84

                ....*
1BX2_B      176 PSVTS 180
Cdd:cd16092  85 TASKS 89
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.17
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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