Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, including T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, including butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. 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" in the other. 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 by strands G, F, C, and C'. Moreover, a C1-set Ig domain contains a short C' strand (three residues) and lacks A' and C" strand. Unlike other Ig domain sets, C2-set structures do not have a D strand. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2322547325  12 VTQRDHFQIITVGSSAKIHCEHDDaSYITILWYRQErhgEKRQLQLIAHSVQGNDPQIE---VKEYSIDRPSVKEASLST 88
Cdd:cd05899     1 VTQSPRYLIKRRGQSVTLRCSQKS-GHDNMYWYRQD---PGKGLQLLFYSYGGGLNEEGdlpGDRFSASRPSLTRSSLTI 76

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2322547325  89 PEQKAEDSAVYFCAA--RGQAETLYFGQGTRLTV 120
Cdd:cd05899    77 KSAEPEDSAVYLCASslGGGADEAYFGPGTRLTV 110

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2322547325  12 VTQRDHFQIITVGSSAKIHCEHDDaSYITILWYRQErhgEKRQLQLIAHSVQGNDPQIE---VKEYSIDRPSVKEASLST 88
Cdd:cd05899     1 VTQSPRYLIKRRGQSVTLRCSQKS-GHDNMYWYRQD---PGKGLQLLFYSYGGGLNEEGdlpGDRFSASRPSLTRSSLTI 76

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2322547325  89 PEQKAEDSAVYFCAA--RGQAETLYFGQGTRLTV 120
Cdd:cd05899    77 KSAEPEDSAVYLCASslGGGADEAYFGPGTRLTV 110

Immunoglobulin C-Type;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2322547325  147 KVTIVCLVTDFYPDHVNLTWSVDGDERTKGVKTKEPDLDKAAkKFSLISRLRITRKEWEKTKEIQCNV 214
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEVTEGVSTTDPLKNSDG-TYFLSSYLTVPASTWESGDVYTCQV 67

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2322547325   19 QIITVGSSAKIHCEHDDASYITILWYRQerhgekrQLQLIAHSvqgndpqievKEYSIDRPSvKEASLSTPEQKAEDSAV 98
Cdd:smart00410   4 VTVKEGESVTLSCEASGSPPPEVTWYKQ-------GGKLLAES----------GRFSVSRSG-STSTLTISNVTPEDSGT 65

                           90       100
                   ....*....|....*....|..
gi 2322547325   99 YFCAARGQAETLYfgQGTRLTV 120
Cdd:smart00410  66 YTCAATNSSGSAS--SGTTLTV 85

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2322547325  12 VTQRDHFQIITVGSSAKIHCEHDDaSYITILWYRQErhgEKRQLQLIAHSVQGNDPQIE---VKEYSIDRPSVKEASLST 88
Cdd:cd05899     1 VTQSPRYLIKRRGQSVTLRCSQKS-GHDNMYWYRQD---PGKGLQLLFYSYGGGLNEEGdlpGDRFSASRPSLTRSSLTI 76

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2322547325  89 PEQKAEDSAVYFCAA--RGQAETLYFGQGTRLTV 120
Cdd:cd05899    77 KSAEPEDSAVYLCASslGGGADEAYFGPGTRLTV 110

Immunoglobulin C1-set domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2322547325 132 VTIFDPSAQELqeKQKVTIVCLVTDFYPDHVNLTWSVDGDERTKGVKTKEPDLDKAAkKFSLISRLRITRKEWEKTKEIQ 211
Cdd:pfam07654   1 VYVFPPSPEEL--GKPNTLTCLVTGFYPPDITVTWLKNGQEVTEGVKTTPPSPNSDW-TYQLSSYLTVTPSDWESGDEYT 77

                  ...
gi 2322547325 212 CNV 214
Cdd:pfam07654  78 CRV 80

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 2322547325 130 PTVTIFDPSAQELQEKQKVTIVCLVTDFYPDHVNLTWSVDGDER-TKGVKTKEPDLDKaAKKFSLISRLRITRKEWEKTK 208
Cdd:cd05768     1 PSVYLLPPPEEELSLNETVTLTCLVKGFYPEDIFVSWLQNGEPLpSADYKTTAPVPES-DGSFFVYSKLNVSTADWNSGD 79

                          90
                  ....*....|....*.
gi 2322547325 209 EIQCNVYFDPLKQNYT 224
Cdd:cd05768    80 VFSCVVGHEALPLQFT 95

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar proteins; The members here are composed of the immunoglobulin (Ig) variable domain of the alpha 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 represents the variable domain of the alpha chain of TCRs and also includes the variable domain of delta chains of 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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2322547325  12 VTQRDHFQIITVGSSAKIHCEHDDASYITILWYRQErHGEKRQLQLIAHSVQGNDpqiEVKEYSI--DRpSVKEASLSTP 89
Cdd:cd04983     1 VTQSPQSLSVQEGENVTLNCNYSTSTFYYLFWYRQY-PGQGPQFLIYISSDSGNK---KKGRFSAtlDK-SRKSSSLHIS 75

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2322547325  90 EQKAEDSAVYFCAARGQAET--LYFGQGTRLTV 120
Cdd:cd04983    76 AAQLSDSAVYFCALSESGGTgkLTFGKGTRLTV 108

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 2322547325 129 PPTVTIFDPSAQELQEKQKVTIVCLVTDFYPDHVNLTWSVDGDERT--KGVKTKEPDLDKaAKKFSLISRLRITRKEWEK 206
Cdd:cd16093     1 PPTVSLHAPSREEFLGNRTATFVCLATGFSPKTISFKWLRNGKEVTssTGAVVEEPKEDG-KTLYSATSFLTITESEWKS 79

                  ....*...
gi 2322547325 207 TKEIQCNV 214
Cdd:cd16093    80 QTEFTCEF 87

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2322547325 148 VTIVCLVTDFYPDHVNLTWSVDGDERTKGVKTKEPDLDKAakKFSLISRLRITRKEWEKTKEIQCNV 214
Cdd:cd21819    18 VTVGCLATDFLPDSITFSWTDDNNSLTTGVKTYPSVLTGG--TYTASSQLQVPESEWKSKENFYCKV 82

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 2322547325  23 VGSSAKIHCE----HDDASYiTILWYRQERhgEKRQLQLIAHSVQGNDPQIEVKEYSI-DRPSVKEASLSTPEQKAEDSA 97
Cdd:pfam07686  10 LGGSVTLPCTysssMSEAST-SVYWYRQPP--GKGPTFLIAYYSNGSEEGVKKGRFSGrGDPSNGDGSLTIQNLTLSDSG 86

                          90       100
                  ....*....|....*....|....
gi 2322547325  98 VYFCAARGQaETLYFGQGTRLTVV 121
Cdd:pfam07686  87 TYTCAVIPS-GEGVFGKGTRLTVL 109

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy epsilon and gamma 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 epsilon and gamma 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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2322547325 129 PPTVTIFDPSAQELQEKQkVTIVCLVTDFYPDHVNLTWsvDGDERTKGVKTKePDLDKAAKKFSLISRLRITRKEWEkTK 208
Cdd:cd21817     1 APSVFPLAPCCKSTNGSS-VTLGCLVTGYFPEPVTVTW--NSGSLTSGVKTF-PAVLQSSGLYTTSSQVTVPSSSWG-SQ 75

                          90
                  ....*....|....*....
gi 2322547325 209 EIQCNVYFDPLKQNYTGTI 227
Cdd:cd21817    76 TFTCNVEHKPSSTKVDKKI 94

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2322547325 130 PTVTIFdPSAQELQEKQKVtIVCLVTDFYPDHVNLTWSVDGDERTKGV 177
Cdd:cd21001     4 PTVTIS-PSRTEALNHHNL-LVCSVTDFYPGQIKVRWFRNDQEETAGV 49

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
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2322547325 128 SPPTVTIFDPSAQElqeKQKVTIVCLVTDFYPDHVNLTWSVDGDERTKGVKTKE 181
Cdd:cd21029     1 VKPRVRLSSRPSPG---DGHLQLSCHVTGFYPRPIEVTWLRDGQEQMDGTQSGG 51

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2322547325 129 PPTVTIFDPSAQELQEKQkvTIVCLVTDFYPDHVNLTWSVDGDERTKGV 177
Cdd:cd05767     2 PPEVTVFPKSPVELGEPN--TLICFVDNFFPPVINVTWLRNGQPVTDGV 48

CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, and mu chains, and CH2 domain (second constant Ig domain of the gheavy chain) in immunoglobulin heavy gamma chain; member of the C1-set of Ig superfamily (IgSF) ; The members here are composed of the third immunoglobulin constant domain (IgC) of the gamma heavy chains and the second immunoglobulin constant domain (IgC) of alpha, epsilon, and 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 2322547325 130 PTVTIFDPSAQELQEKQKVTIVCLVTDFYP-DHVNLTWSVDGDERTKGVKTKEPDLDKAAkkFSLISRLRITRKEWEKTK 208
Cdd:cd07696     1 VSVFLIPPSPKDLFLTKSAKVTCLVVDLTSiEEVNVTWSREDGNEVLASTTNPEKHYNAT--LSVVSTLTVCADDWDNGK 78

                  ....*.
gi 2322547325 209 EIQCNV 214
Cdd:cd07696    79 TFKCKV 84

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 2322547325  22 TVGSSAKIHCEHDDASY--ITILWYrQERHGeKRQLQLIAHSVQGNDPQIEVKEYSIDRPSvkeASLSTPEQKAEDSAVY 99
Cdd:cd04984    11 SPGETVTITCTGSSGNIsgNYVNWY-QQKPG-SAPRYLIYEDKHRPSGIPDRFSGSKSGNT---ASLTISGAQTEDEADY 85

                          90       100
                  ....*....|....*....|.
gi 2322547325 100 FCAArGQAETLYFGQGTRLTV 120
Cdd:cd04984    86 YCQV-WDSNSYVFGGGTKLTV 105

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
                  ....*....|....*....|....*....|....*....|....*....
gi 2322547325 129 PPTVTIFDPSAQELqeKQKVTIVCLVTDFYPDHVNLTWSVDGDERTKGV 177
Cdd:cd21004     2 PPRVTVLPKSRVEL--GQPNILICIVDNIFPPVINITWLRNGQTVTEGV 48

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.

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                  ....*....|....*....|....*....|....*....|....*...
gi 2322547325 130 PTVTIFDPSAQELQEKQkvTIVCLVTDFYPDHVNLTWSVDGDERTKGV 177
Cdd:cd20998     7 PTVTVYPTKTQPLEHHN--LLVCSVSDFYPGNIEVRWFRNGKEEKTGI 52

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.

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                  ....*....|....*....|....*....|....*....|....*....|....
gi 2322547325 129 PPTVTIFDPSAQElqekQKVTIVCLVTDFYPDHVNLTWSVDGDERTKGVKTKEP 182
Cdd:cd07698     2 PPKVHVTHHPRSD----GESTLRCWALGFYPAEITLTWQRDGEDQTQDMELVET 51

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.

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                  ....*....|....*....|....*....|....
gi 2322547325  92 KAEDSAVYFCaARGQAETL-----YFGQGTRLTV 120
Cdd:cd04981    85 TSEDTAVYYC-ARGLGGYGysyfdYWGQGTTVTV 117

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2322547325 130 PTVTIFDPSAQELQEKQkvTIVCLVTDFYPDHVNLTWSVDGDERTKGVkTKEPDLDKAAKKFSLISRL 197
Cdd:cd21008     3 PEVTVFPKSPVTLGQPN--TLICLVDNIFPPVINITWLSNGHSVTEGV-SETSFLSKSDHSFLKISYL 67

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

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2322547325 143 QEKQKVTIVCLVTDFYPDHVNLTWSVDGDERTKGVKTKE--PDLDKAAKKF-SLISRLritrkewEKTKEIQCNVYFDPL 219
Cdd:cd21018    15 RSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVEtrPAGDGTFQKWaSVVVPL-------GKEQNYTCRVYHEGL 87

                  ....*
gi 2322547325 220 KQNYT 224
Cdd:cd21018    88 PEPLT 92