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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459 143 FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPLKEqpalNDSRYCLSSRLRVSATF 222
Cdd:cd05769   1 TPPTVALFPPSEAEIRNKRKATLVCLATGFYPDHVSLSWKVNGKEVKDGVATDPQALRE----NTSTYSLSSRLRVSATE 76

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 44887459 223 WQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW 262
Cdd:cd05769  77 WFNPRNTFTCIVKFYGGTDTDTWTQGIAGPVTCGVSAEEL 116

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459 143 FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPLKEqpalNDSRYCLSSRLRVSATF 222
Cdd:cd05769   1 TPPTVALFPPSEAEIRNKRKATLVCLATGFYPDHVSLSWKVNGKEVKDGVATDPQALRE----NTSTYSLSSRLRVSATE 76

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 44887459 223 WQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW 262
Cdd:cd05769  77 WFNPRNTFTCIVKFYGGTDTDTWTQGIAGPVTCGVSAEEL 116

Immunoglobulin C1-set domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459   147 VAVFEPSEAEISHtqKATLVCLATGFYPDHVELSWWVNGKEVHSGV-STDPQPLKeqpalnDSRYCLSSRLRVSATFWqN 225
Cdd:pfam07654   1 VYVFPPSPEELGK--PNTLTCLVTGFYPPDITVTWLKNGQEVTEGVkTTPPSPNS------DWTYQLSSYLTVTPSDW-E 71

                          90
                  ....*....|....
gi 44887459   226 PRNHFRCQVQFYGL 239
Cdd:pfam07654  72 SGDEYTCRVEHEGL 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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459    25 QTPKFRILKIGQSMTLQCT----QDMNHNYMYWYRQDPGMGLK-LIYYSVgaGITDKGEVPNGYNVSRSTTE-DFPLRLE 98
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTysssMSEASTSVYWYRQPPGKGPTfLIAYYS--NGSEEGVKKGRFSGRGDPSNgDGSLTIQ 78

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 44887459    99 LAAPSQTSVYFCAsssrtsgTWGIYEQYFGPGTRLTVT 136
Cdd:pfam07686  79 NLTLSDSGTYTCA-------VIPSGEGVFGKGTRLTVL 109

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459 143 FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPLKEqpalNDSRYCLSSRLRVSATF 222
Cdd:cd05769   1 TPPTVALFPPSEAEIRNKRKATLVCLATGFYPDHVSLSWKVNGKEVKDGVATDPQALRE----NTSTYSLSSRLRVSATE 76

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 44887459 223 WQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW 262
Cdd:cd05769  77 WFNPRNTFTCIVKFYGGTDTDTWTQGIAGPVTCGVSAEEL 116

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459  23 VTQTPKFRILKIGQSMTLQCTQDM--NHNYMYWYRQDPGMGLKLIYYSVGAGITDKGEVPNGYNVSRSTTEDFPLRLELA 100
Cdd:cd00099   1 VTQSPRSLSVQEGESVTLSCEVSSsfSSTYIYWYRQKPGQGPEFLIYLSSSKGKTKGGVPGRFSGSRDGTSSFSLTISNL 80

                        90       100       110
                ....*....|....*....|....*....|....*
gi 44887459 101 APSQTSVYFCASssrtSGTWGIYEQYFGPGTRLTV 135
Cdd:cd00099  81 QPEDSGTYYCAV----SESGGTDKLTFGSGTRLTV 111

Immunoglobulin C-Type;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459    162 KATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPqPLKEqpalNDSRYCLSSRLRVSATFWqNPRNHFRCQVQFYGLSE 241
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEVTEGVSTTD-PLKN----SDGTYFLSSYLTVPASTW-ESGDVYTCQVTHEGLKE 74

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459 144 PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPLKEQpalNDSRYCLSSRLRVSATFW 223
Cdd:cd16093   1 PPTVSLHAPSREEFLGNRTATFVCLATGFSPKTISFKWLRNGKEVTSSTGAVVEEPKED---GKTLYSATSFLTITESEW 77

                        90
                ....*....|....*....
gi 44887459 224 QNPRnHFRCQVQFYGLSEN 242
Cdd:cd16093  78 KSQT-EFTCEFKHKGEIVE 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459 145 PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPLKEqpalNDSRYCLSSRLRVSATFWQ 224
Cdd:cd05768   1 PSVYLLPPPEEELSLNETVTLTCLVKGFYPEDIFVSWLQNGEPLPSADYKTTAPVPE----SDGSFFVYSKLNVSTADWN 76

                        90
                ....*....|
gi 44887459 225 NpRNHFRCQV 234
Cdd:cd05768  77 S-GDVFSCVV 85

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459  23 VTQTPKFRILKIGQSMTLQCT--QDMNHNYMYWYRQDPGMGLKLIYYSVGAGITDkgeVPNGYNVSRSTTeDFPLRLELA 100
Cdd:cd04980   3 MTQSPASLSVSPGERVTISCKasQSISSNYLAWYQQKPGQAPKLLIYYASTLHSG---VPSRFSGSGSGT-DFTLTISSV 78

                        90       100       110
                ....*....|....*....|....*....|....*
gi 44887459 101 APSQTSVYFCASSSRTSGTwgiyeqyFGPGTRLTV 135
Cdd:cd04980  79 EPEDAAVYYCQQGYTFPYT-------FGGGTKLEI 106

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here are composed of the immunoglobulin (Ig) variable (V) 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 antigens as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma/delta TCRs recognize intact protein antigens directly without antigen processing and recognize 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 the standard Ig superfamily V-set AGFCC'C"/DEB domain topology.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459  23 VTQTPKFRILKIGQSMTLQCT---QDMNHNYMYWYRQDPGMGL-KLIYY-SVGAGITDKGEVPNGYNVSR-STTEDFPLR 96
Cdd:cd04982   1 LEQPQLSITREESKSVTISCKvsgIDFSTTYIHWYRQKPGQALeRLLYVsSTSAVRKDSGKTKNKFEARKdVGKSTSTLT 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 44887459  97 LELAAPSQTSVYFCASSSRTSGTWgiyEQYFGPGTRLTVT 136
Cdd:cd04982  81 ITNLEKEDSATYYCAYWESGSGYY---IKVFGSGTKLIVT 117

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459 144 PPEVAVFEPSEAEishtQKATLVCLATGFYPDHVELSWWVNGKEVhsgvsTDPQPLKE-QPAlNDSRYCLSSRLRVSATF 222
Cdd:cd07698   2 PPKVHVTHHPRSD----GESTLRCWALGFYPAEITLTWQRDGEDQ-----TQDMELVEtRPN-GDGTFQKWAAVVVPSGE 71

                        90
                ....*....|....*....
gi 44887459 223 WQNprnhFRCQVQFYGLSE 241
Cdd:cd07698  72 EQR----YTCHVQHEGLPE 86

Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the immunoglobulin (Ig) heavy chain (H), 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. 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 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 can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459  33 KIGQSMTLQCTQD---MNHNYMYWYRQDPGMGLKLI--YYSVGAGITDKGEVPNGYNVSRSTTED-FPLRLELAAPSQTS 106
Cdd:cd04981  11 KPGQSLKLSCKASgftFTSYGMGWVRQAPGKGLEWIglIYPGGGDTYYADSFKGRFTITRDTSKStAYLQLNSLTSEDTA 90

                        90       100       110
                ....*....|....*....|....*....|
gi 44887459 107 VYFCASSSRTSGTWGIYeqYFGPGTRLTVT 136
Cdd:cd04981  91 VYYCARGLGGYGYSYFD--YWGQGTTVTVS 118

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459 144 PPEVAVFEPSEAEISHTQkatLVCLATGFYPDHVELSWWVNGKEVHSGVSTD---PQPlkeqpalnDSRYclssRLRVSA 220
Cdd:cd21029   2 KPRVRLSSRPSPGDGHLQ---LSCHVTGFYPRPIEVTWLRDGQEQMDGTQSGgilPNH--------DGTY----QLRKTL 66

                        90       100
                ....*....|....*....|..
gi 44887459 221 TFWQNPRNHFRCQVQFYGLSEN 242
Cdd:cd21029  67 DIAPGEGAGYSCRVDHSSLKQD 88

Gammadelta T-cell antigen receptor, variable (V) domain; The members here are composed of the immunoglobulin (Ig) variable (V) domain of the 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459  30 RILKIGQSMTLQCT---QDMNHNYMYWYRQDPGMGLKLIYYS---VGAGITD--KGEVPNGYNVSrsttedfplRLELAA 101
Cdd:cd20988   8 VTVSVGKPVTLKCSmkgEAISNYYINWYRKTQGNTMTFIYREggiYGPGFKDnfRGDIDSSNNLA---------VLKILE 78

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 44887459 102 PSQ--TSVYFCASSsrTSGTWGIYEQY-FGPGTRLTV 135
Cdd:cd20988  79 ASErdEGSYYCASD--TPGGGREYDPLiFGKGTYLTV 113

Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, lambda type, variable (V) domain. 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. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459  23 VTQTPKFRIlKIGQSMTLQCT---QDMNHNYMYWYRQDPGMGLKLIYY---SVGAGItdkgevPNGYNVSRSTTeDFPLR 96
Cdd:cd04984   2 LTQPSSLSV-SPGETVTITCTgssGNISGNYVNWYQQKPGSAPRYLIYedkHRPSGI------PDRFSGSKSGN-TASLT 73

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 44887459  97 LELAAPSQTSVYFCASSSRTSGTwgiyeqyFGPGTRLTV 135
Cdd:cd04984  74 ISGAQTEDEADYYCQVWDSNSYV-------FGGGTKLTV 105

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
                ....*....|....*....|....*....|....*....|....*...
gi 44887459 145 PEVAVFEPSEAEISHTQkaTLVCLATGFYPDHVELSWWVNGKEVHSGV 192
Cdd:cd21000   4 PKVTVYPAKTQPLQHHN--LLVCSVNGFYPGSIEVRWFRNGQEEKAGV 49

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459 145 PEVAVFEPSEAEIShtQKATLVCLATGFYPDHVELSWWVNGKEVHSGVStdpqplkEQPALNDSRYclsSRLRVS-ATFW 223
Cdd:cd21008   3 PEVTVFPKSPVTLG--QPNTLICLVDNIFPPVINITWLSNGHSVTEGVS-------ETSFLSKSDH---SFLKISyLTFL 70

                        90
                ....*....|....*...
gi 44887459 224 QNPRNHFRCQVQFYGLSE 241
Cdd:cd21008  71 PSADDIYDCKVEHWGLDK 88

CH1 domain (first 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 first immunoglobulin constant-1 set domain of alpha chains. It belongs to a family composed of the first immunoglobulin constant-1 set 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 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 44887459 165 LVCLATGFYPDHVELSWWVNGKevhsGVSTDPQPlkeqPALNDS-RYCLSSRLRVSATFWQNPRNhFRCQVQFYGLSEN 242
Cdd:cd21818  20 IGCLVQGFFPEPVNVTWNYSGK----GGTARNFP----AMLASGgRYTQSSQLTLPADQCPEGEA-YKCSVQHYSPSQD 89

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459 144 PPEVAVFEPseaEISHTQKAT-LVCLATGFYPDHVELSWWVNGKEV--HSGVSTDPQPlkeqpalN-DSRYCLSSRLRVS 219
Cdd:cd21002   3 PPSVRVAPT---TPFNTREPVmLACHVWGFYPADVTITWLKNGDPVapHSSAPKTAQP-------NgDWTYQTQVTLAVT 72

                        90       100
                ....*....|....*....|..
gi 44887459 220 ATFWQNprnhFRCQVQFYGLSE 241
Cdd:cd21002  73 PSPGDT----YTCSVQHASLPE 90

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459  23 VTQTPKFRILKIGQSMTLQCTQDMNHN--YMYWYRQDPGMGLKLIYYsvgaGITDKGEVPNG-YNVS-RSTTEDFPLRLE 98
Cdd:cd07706   2 VTQAQPDVSVQVGEEVTLNCRYETSWTnyYLFWYKQLPSGEMTFLIR----QDSSEQNAKSGrYSVNfQKAQKSISLTIS 77

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 44887459  99 LAAPSQTSVYFCASSSRTSGTWGIyeqyFGPGTRLTV 135
Cdd:cd07706  78 ALQLEDSAKYFCALSLPYDTDKLI----FGKGTRLTV 110

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459 144 PPEVAVFEPSEAEIShtQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYClssrlrvsaTFW 223
Cdd:cd21007   2 PPEVTVLTNSPVELR--EPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYL---------PFL 70

                        90
                ....*....|....*...
gi 44887459 224 QNPRNHFRCQVQFYGLSE 241
Cdd:cd21007  71 PSTEDVYDCRVEHWGLDE 88

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459 151 EPSEAEISHTQKA----TLVCLATGFYPDHVELSWWVNGKEvhsgVSTDPQPLKEQPAlNDSRYCLSSRLRVSATFWQNp 226
Cdd:cd21014   3 DPPKAHVTHHPRSygavTLRCWALGFYPADITLTWQLNGEE----LTQDMELVETRPA-GDGTFQKWASVVVPLGKEQN- 76

                        90
                ....*....|....*
gi 44887459 227 rnhFRCQVQFYGLSE 241
Cdd:cd21014  77 ---YTCHVNHEGLPE 88

Immunoglobulin constant (IgC)-like domain of antigen receptor Cluster of Differentiation (CD) 80; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin constant (IgC)-like domain of the antigen receptor Cluster of Differentiation (CD) 80. CD80 (also known as glycoprotein B7-1) and CD86 (also known as glycoprotein B7-2) are expressed on antigen-presenting cells and deliver the co-stimulatory signal through CD28 and CTLA-4 (CD152) on T cells. signaling through CD28 augments the T-cell response, whereas CTLA-4 signaling attenuates it. CD80 contains two Ig-like domains, an amino-terminal immunoglobulin variable (IgV)-like domain characteristic of adhesion molecules, and a membrane proximal immunoglobulin constant (IgC)-like domain similar to the constant domains of antigen receptors. Members of the Ig 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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459 143 FP-PEVAVFEPSEAEIShtqkaTLVCLATGFYPDHvELSWWVNGKE---VHSGVSTDPQplkeqpalnDSRYCLSSRLRV 218
Cdd:cd16083   1 FPvPSITEFGNPSPNIK-----RIICSTSGGFPEP-RLSWLENGEElnaINTTVSQDPE---------TELYTVSSELDF 65

                        90       100       110
                ....*....|....*....|....*....|.
gi 44887459 219 SATfwqnpRNH-FRCQVQfYG---LSENDEW 245
Cdd:cd16083  66 NVT-----YNHsIVCLIK-YGdsrVSKNFTW 90

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 44887459 145 PEVAVFEPSEAEISHTQkaTLVCLATGFYPDHVELSWWVNGKEVHSGV 192
Cdd:cd20998   7 PTVTVYPTKTQPLEHHN--LLVCSVSDFYPGNIEVRWFRNGKEEKTGI 52

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin delta 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 delta 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 44887459 165 LVCLATGFYPDHVELSWWVngkevhsGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQnpRNHFRCQVQ 235
Cdd:cd16092  22 LACLITGYHPTSVTVTWYM-------GTQSQPQRTFPEIQRRDSYYMTSSQLSTPLQQWR--QGEYKCVVQ 83

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'.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 44887459 151 EPSEAEISHTQK----ATLVCLATGFYPDHVELSWWVNGKEV 188
Cdd:cd21012   4 DPPKTHVTHHPRpegyVTLRCWALGFYPAHITLTWQLNGEEL 45

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459 145 PEVAVFEpsEAEISHTQKATLVCLATGFYPDHVELSWWvngKEVHSGvsTDPQPLKEQPALN------DSRYCLSSRLRV 218
Cdd:cd05771   1 PRVRLSP--KNLVKPDLPQTLSCHIAGYYPLDVDVEWL---REEPGG--SESQVSRDGVSLSshrqsvDGTYSISSYLTL 73

                        90       100
                ....*....|....*....|...
gi 44887459 219 SATFWQNPRNhFRCQVQFYGLSE 241
Cdd:cd05771  74 EPGTENRGAT-YTCRVTHVSLEE 95

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44887459     33 KIGQSMTLQCT-QDMNHNYMYWYRQdpgmGLKLIYYsvgagitdkgevPNGYNVSRSTTeDFPLRLELAAPSQTSVYFCA 111
Cdd:smart00410   7 KEGESVTLSCEaSGSPPPEVTWYKQ----GGKLLAE------------SGRFSVSRSGS-TSTLTISNVTPEDSGTYTCA 69

                           90       100
                   ....*....|....*....|....
gi 44887459    112 SSSRtsgtwgiYEQYFGpGTRLTV 135
Cdd:smart00410  70 ATNS-------SGSASS-GTTLTV 85

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 44887459 144 PPEVAVFEPSEAEIShtQKATLVCLATGFYPDHVELSWWVNGKEVHSGVS 193
Cdd:cd21004   2 PPRVTVLPKSRVELG--QPNILICIVDNIFPPVINITWLRNGQTVTEGVA 49