Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, kappa type, variable (V) domain. This group contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology. 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 (CL) and a variable domain (VL). There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: 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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L        2 IVLTQSPASLAVSLGQRATISCRASESVDSYgnsFMHWYQQKPGQPPILLISRASNLESGIPARFSGSGSRTDFTLTINP 81
Cdd:cd04980   1 IVMTQSPASLSVSPGERVTISCKASQSISSN---YLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISS 77

                        90       100
                ....*....|....*....|....*....
5X2P_L       82 VEADDFATYYCQQTNEDPRTFGGGTKLEI 110
Cdd:cd04980  78 VEPEDAAVYYCQQGYTFPYTFGGGTKLEI 106

Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, kappa type, variable (V) domain. This group contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology. 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 (CL) and a variable domain (VL). There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: 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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L        2 IVLTQSPASLAVSLGQRATISCRASESVDSYgnsFMHWYQQKPGQPPILLISRASNLESGIPARFSGSGSRTDFTLTINP 81
Cdd:cd04980   1 IVMTQSPASLSVSPGERVTISCKASQSISSN---YLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISS 77

                        90       100
                ....*....|....*....|....*....
5X2P_L       82 VEADDFATYYCQQTNEDPRTFGGGTKLEI 110
Cdd:cd04980  78 VEPEDAAVYYCQQGYTFPYTFGGGTKLEI 106

Immunoglobulin C1-set domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L        119 VSIFPPSSEQLtSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVlNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTC 198
Cdd:pfam07654   1 VYVFPPSPEEL-GKPNTLTCLVTGFYPPDITVTWLKNGQEVTEGV-KTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTC 78

                  ....*..
5X2P_L        199 EATHKTS 205
Cdd:pfam07654  79 RVEHEGL 85

Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L          6 QSPASLAVSLGQRATISCRASESVdSYGNSFMHWYQQKPGQPPILLISRASNL--ESGIPARFSGSG--SRTDFTLTINP 81
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYSSSM-SEASTSVYWYRQPPGKGPTFLIAYYSNGseEGVKKGRFSGRGdpSNGDGSLTIQN 79

                          90       100
                  ....*....|....*....|....*....
5X2P_L         82 VEADDFATYYCQQTNEDPRTFGGGTKLEI 110
Cdd:pfam07686  80 LTLSDSGTYTCAVIPSGEGVFGKGTRLTV 108

Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, kappa type, variable (V) domain. This group contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology. 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 (CL) and a variable domain (VL). There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: 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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L        2 IVLTQSPASLAVSLGQRATISCRASESVDSYgnsFMHWYQQKPGQPPILLISRASNLESGIPARFSGSGSRTDFTLTINP 81
Cdd:cd04980   1 IVMTQSPASLSVSPGERVTISCKASQSISSN---YLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISS 77

                        90       100
                ....*....|....*....|....*....
5X2P_L       82 VEADDFATYYCQQTNEDPRTFGGGTKLEI 110
Cdd:cd04980  78 VEPEDAAVYYCQQGYTFPYTFGGGTKLEI 106

Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin variable domain (IgV). The IgV family contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology, and are components of immunoglobulin (Ig) and T cell receptors. 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. Within the variable domain, there are regions of even more variability called the hypervariable or complementarity-determining regions (CDRs) which are responsible for antigen binding. A predominant feature of most Ig domains is the disulfide bridge connecting 2 beta-sheets with a tryptophan residue packed against the disulfide bond. Ig superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Typically, the V-set domains have A, B, E and, D strands in one sheet and A', G, F, C, C', and C" strands in the other.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L        4 LTQSPASLAVSLGQRATISCRASesvDSYGNSFMHWYQQKPGQPPILLISRASNLES---GIPARFSGSGSR-TDFTLTI 79
Cdd:cd00099   1 VTQSPRSLSVQEGESVTLSCEVS---SSFSSTYIYWYRQKPGQGPEFLIYLSSSKGKtkgGVPGRFSGSRDGtSSFSLTI 77

                        90       100       110
                ....*....|....*....|....*....|....
5X2P_L       80 NPVEADDFATYYCQQT---NEDPRTFGGGTKLEI 110
Cdd:cd00099  78 SNLQPEDSGTYYCAVSesgGTDKLTFGSGTRLTV 111

Immunoglobulin C1-set domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L        119 VSIFPPSSEQLtSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVlNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTC 198
Cdd:pfam07654   1 VYVFPPSPEEL-GKPNTLTCLVTGFYPPDITVTWLKNGQEVTEGV-KTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTC 78

                  ....*..
5X2P_L        199 EATHKTS 205
Cdd:pfam07654  79 RVEHEGL 85

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'.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L      118 TVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTdQDSKDSTYSMSSTLTLTKDEYERHNSYT 197
Cdd:cd00098   1 TVTLLPPSPEEKGGGKVTLVCLVSGFYPKDITVTWLKNGVPLTSGVSTSSP-VEPNDGTYSVTSSLTVPPSDWDEGATYT 79

                        90
                ....*....|....*.
5X2P_L      198 CEATHKTSTSPIVKSF 213
Cdd:cd00098  80 CVVTHESLKSPLSKTW 95

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L      117 PTVSIFPPSSEQLTSGG-ASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 195
Cdd:cd05768   1 PSVYLLPPPEEELSLNEtVTLTCLVKGFYPEDIFVSWLQNGEPLPSADYKTTAPVPESDGSFFVYSKLNVSTADWNSGDV 80

                        90       100
                ....*....|....*....|..
5X2P_L      196 YTCEATHKTSTSPIV-KSFNRN 216
Cdd:cd05768  81 FSCVVGHEALPLQFTqKSIDKS 102

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here are composed of the immunoglobulin (Ig) variable 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 alpha chain of alpha/beta TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens directly without antigen processing and recognize MHC independently of the bound peptide. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L        4 LTQSPASLAVSLGQRATISCRASESVDSygnsfMHWYQQKPGQPPILLI---SRASNLESGIPA-RFSGSG-SRTDFTLT 78
Cdd:cd05899   1 VTQSPRYLIKRRGQSVTLRCSQKSGHDN-----MYWYRQDPGKGLQLLFysyGGGLNEEGDLPGdRFSASRpSLTRSSLT 75

                        90       100       110
                ....*....|....*....|....*....|...
5X2P_L       79 INPVEADDFATYYC---QQTNEDPRTFGGGTKL 108
Cdd:cd05899  76 IKSAEPEDSAVYLCassLGGGADEAYFGPGTRL 108

Immunoglobulin V-Type;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L          19 ATISCRASESvdSYGNSFMHWYQQKPGQPPILLISRASN----LESGIPARFSGSG--SRTDFTLTINPVEADDFATYYC 92
Cdd:smart00406   2 VTLSCKFSGS--TFSSYYVSWVRQPPGKGLEWLGYIGSNgssyYQESYKGRFTISKdtSKNDVSLTISNLRVEDTGTYYC 79

                   ..
5X2P_L          93 QQ 94
Cdd:smart00406  80 AV 81

Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L           8 PASLAVSLGQRATISCRASesvdSYGNSFMHWYQQKPgqppILLISrasnlesgiPARFSGSGSRTDFTLTINPVEADDF 87
Cdd:smart00410   1 PPSVTVKEGESVTLSCEAS----GSPPPEVTWYKQGG----KLLAE---------SGRFSVSRSGSTSTLTISNVTPEDS 63

                           90       100
                   ....*....|....*....|...
5X2P_L          88 ATYYCQQTNEDPRTFgGGTKLEI 110
Cdd:smart00410  64 GTYTCAATNSSGSAS-SGTTLTV 85

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here are composed of the immunoglobulin (Ig) variable (V) domain of the delta 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. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L        5 TQSPASLAVSLGQRATISCRASESVDSYgnsFMHWYQQKPGQPPILLISRASNLESGIPARFSGSGSRTD--FTLTINPV 82
Cdd:cd07706   3 TQAQPDVSVQVGEEVTLNCRYETSWTNY---YLFWYKQLPSGEMTFLIRQDSSEQNAKSGRYSVNFQKAQksISLTISAL 79

                        90       100       110
                ....*....|....*....|....*....|.
5X2P_L       83 EADDFATYYCQQT---NEDPRTFGGGTKLEI 110
Cdd:cd07706  80 QLEDSAKYFCALSlpyDTDKLIFGKGTRLTV 110

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L      117 PTVSIFPPSSEQLTSGGAsVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSkDSTYsmsSTLTLTKDEYERHNSY 196
Cdd:cd21000   4 PKVTVYPAKTQPLQHHNL-LVCSVNGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG-DWTF---QTLVMLETVPRSGEVY 78

                        90
                ....*....|...
5X2P_L      197 TCEATHKTSTSPI 209
Cdd:cd21000  79 TCQVEHPSVTSPL 91

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'.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L      116 APTVSIFppSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVlNSWTDQDSKDSTYSMSSTLTLTKDEYErhnS 195
Cdd:cd21029   2 KPRVRLS--SRPSPGDGHLQLSCHVTGFYPRPIEVTWLRDGQEQMDGT-QSGGILPNHDGTYQLRKTLDIAPGEGA---G 75

                        90
                ....*....|....*
5X2P_L      196 YTCEATHKTSTSPIV 210
Cdd:cd21029  76 YSCRVDHSSLKQDLI 90

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L      117 PTVSIFPPSSEQLTSGgASVVCFLNNFYPKDINVKWKIDGSERQNGVlNSWTDQDSKDSTYSMSSTLTLTKdeyERHNSY 196
Cdd:cd05766   4 PSVKVSPTKTGPLEHP-NLLVCSVTGFYPAEIEVKWFRNGQEETAGV-VSTELIPNGDWTFQILVMLETTP---RRGDVY 78

                        90
                ....*....|...
5X2P_L      197 TCEATHKTSTSPI 209
Cdd:cd05766  79 TCQVEHSSLQSPL 91

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, epsilon, gamma, and mu chains; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin constant-1 set domain of alpha, delta, 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 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. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L      116 APTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 195
Cdd:cd04985   1 APTVFPLQSATKSQSNGPVALGCLISDYFPESITVSWQKNTNSITSGFTRTFPVVLRSGGDYSCSSQLTVPLQEWNSGEV 80

                        90
                ....*....|..
5X2P_L      196 YTCEATHKTSTS 207
Cdd:cd04985  81 YKCQVQHSASNS 92

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L      122 FPPS---SEQLTSGG--ASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDqdSKDSTYSMSSTLTLTKDEYERHNSY 196
Cdd:cd16085   1 VPPTlevTQQPTMVWnqVNVTCQVEKFYPQRLQLTWLENGNVSRTETPSTLTV--NKDGTYNWTSWLLVNVSAHREDVVL 78

                ....*.
5X2P_L      197 TCEATH 202
Cdd:cd16085  79 TCQVEH 84

T cell receptor (TCR) gamma chain constant immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the 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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L      116 APTVSIFPPSS-EQLTSGGASVVCFLNNFYPKDINVKWKIDGSER--QNGVLNSWTDQDskdsTYSMSSTLTLTKDEYEr 192
Cdd:cd07697   1 SPKPTIFLPSIaETEKQKAGTYLCLLENFFPDVIKIHWREKKSDTilESQEGNTEKTKD----TYMKFSWLTVPKKSLG- 75

                        90       100
                ....*....|....*....|
5X2P_L      193 hNSYTCEATHKtSTSPIVKS 212
Cdd:cd07697  76 -KEHRCIYKHE-NNKNGVKQ 93

Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The members here are composed of the immunoglobulin (Ig)-like domain in Cluster of Differentiation (CD) 8 beta. The CD8 glycoprotein plays an essential role in the control of T-cell selection, maturation, and the T-cell receptor (TCR)-mediated response to peptide antigen. CD8 is comprised of alpha and beta subunits and is expressed as either an alpha/alpha or alpha/beta dimer. Both dimeric isoforms can serve as a coreceptor for T cell activation and differentiation, however they have distinct physiological roles, different cellular distributions, unique binding partners, etc. Each CD8 subunit is comprised of an extracellular domain containing a V-type Ig-like domain, a single pass transmembrane portion, and a short intracellular domain. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L        4 LTQSPASLAVSLGQRATISCrasESVDSYGNSFMHWYQQKPGQPPillISRASNLESGIPAR--------------FSGS 69
Cdd:cd07700   1 LLQTPGSLLVQTNQTVKMSC---EAKTSPKNTRIYWLRQRQAPSK---DSHFEFLASWDPSKgivygegvdqekliILSD 74

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
5X2P_L       70 GSRTDFTLTINPVEADDFATYYCQQTNEDPRTFGGGTKLEI 110
Cdd:cd07700  75 SDSSRYILSLMSVKPEDSGTYFCMTVGSPELIFGTGTKLSV 115

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L      116 APTVSIF-PPSSEqltsGGASVVCFLNNFYPKDINVKWKIDGSE----------RQNGvlnswtdqdskDSTYSMSSTLT 184
Cdd:cd07698   2 PPKVHVThHPRSD----GESTLRCWALGFYPAEITLTWQRDGEDqtqdmelvetRPNG-----------DGTFQKWAAVV 66

                        90       100
                ....*....|....*....|....*.
5X2P_L      185 LTKDEYERhnsYTCEATHKTSTSPIV 210
Cdd:cd07698  67 VPSGEEQR---YTCHVQHEGLPEPLT 89

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy mu chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin constant-1 set domain of mu chains. It belongs to a family composed of the first immunoglobulin constant-1 set domain of alpha, delta, 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 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. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L      116 APTVsiFP-PSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQdsKDSTYSMSSTLTLTKDEYERHN 194
Cdd:cd21819   1 APTL--FPlVSCGSSTSDPVTVGCLATDFLPDSITFSWTDDNNSLTTGVKTYPSVL--TGGTYTASSQLQVPESEWKSKE 76

                ....*...
5X2P_L      195 SYTCEATH 202
Cdd:cd21819  77 NFYCKVEH 84

Immunoglobulin domain; This family contains immunoglobulin-like domains.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L          3 VLTQSPASLAVSLGQRATISCRASesvdSYGNSFMHWYqqKPGQPPILLISRASNLESGiparfsgsgsrtDFTLTINPV 82
Cdd:pfam13927   3 VITVSPSSVTVREGETVTLTCEAT----GSPPPTITWY--KNGEPISSGSTRSRSLSGS------------NSTLTISNV 64

                          90
                  ....*....|....
5X2P_L         83 EADDFATYYCQQTN 96
Cdd:pfam13927  65 TRSDAGTYTCVASN 78

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L      116 APTVSIFPpSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSwTDQDSKDSTYSMSSTLTLTKDEyerHNS 195
Cdd:cd21006   2 APQATVFP-KSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVTDGVYET-SFLVNRDHSFHKLSYLTFIPSD---DDI 76

                        90
                ....*....|....*....
5X2P_L      196 YTCEATHKTSTSPIVKSFN 214
Cdd:cd21006  77 YDCKVEHWGLEEPVLKHWE 95

Immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha and beta; member of the I-set of IgSF domains; The members here are composed of the immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha (also known as cluster of differentiation (CD) 140a), and beta (also known as CD140b). PDGF is a potent mitogen for connective tissue cells. PDGF-stimulated processes are mediated by three different PDGFs (PDGF-A,PDGF-B, and PDGF-C). PDGFRalpha binds to all three PDGFs, whereas the PDGFRbeta binds only to PDGF-B. PDGFRs alpha and beta have similar organization: an extracellular component with five Ig-like domains, a transmembrane segment, and a cytoplasmic portion having protein tyrosine kinase activity. In mice, PDGFRalpha and PDGFRbeta are essential for normal development.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
5X2P_L      148 INVKWKIDGSERQNGVLNSwtdQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFN 214
Cdd:cd05861  32 VDLEWTYPGKESGRGIEPV---EEFKVPPYHLVYTLTIPSATLEDSGTYECAVTEATNDHQDEKKIN 95

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L      111 KRADAAPTVSIFPPSSEQltsgGASVVCFLNNFYPKDINVKWKIDGsERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEY 190
Cdd:cd21026   1 QRADPPKTHVTHHPISDH----EATLRCWALGFYPAEITLTWQRDG-EDQTQDTELVETRPAGDRTFQKWAAVVVPSGEE 75

                        90
                ....*....|....*....
5X2P_L      191 ERhnsYTCEATHKTSTSPI 209
Cdd:cd21026  76 QR---YTCHVQHEGLPKPL 91

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L      123 PP---SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERhnsYTCE 199
Cdd:cd21021   4 PPlvkVTHHVTSSVTTLRCRALNYYPQNITMKWLKDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQR---YTCQ 80

                        90
                ....*....|.
5X2P_L      200 ATHKTSTSPIV 210
Cdd:cd21021  81 VEHPGLDQPLI 91

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L      117 PTVSIFPPSSEQLTSGGaSVVCFLNNFYPKDINVKWKIDGSERQNGVlnSWTDQDSK-DSTYSMSSTLTLTKDEYErhnS 195
Cdd:cd21008   3 PEVTVFPKSPVTLGQPN-TLICLVDNIFPPVINITWLSNGHSVTEGV--SETSFLSKsDHSFLKISYLTFLPSADD---I 76

                        90
                ....*....|....*.
5X2P_L      196 YTCEATHKTSTSPIVK 211
Cdd:cd21008  77 YDCKVEHWGLDKPLLK 92

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin constant-1 set domain (IgC) of alpha 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. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5X2P_L      117 PTVSIFPPSSEQLTSG-GASVVCFLNnfypkdinvkwkidGSERQNGVLNSWTDQDSKDST-----------YSMSSTLT 184
Cdd:cd04986   2 PRLSLQRPALEDLLLGsNASLTCTLS--------------GLKDPEGATFTWEPSGGKEAIqgpperdscgcYSVSSVLP 67

                        90       100
                ....*....|....*....|....*...
5X2P_L      185 LTKDEYERHNSYTCEATHKTSTSPIVKS 212
Cdd:cd04986  68 GCAEPWNSGDTFSCTVTHPESKGTLTAT 95