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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66794516 250 LSLQRPALEDLLLGSDASITCTLNGLRDPEGAVFTWEPSTGKDAVQKKAVQNSCGCYSVSSVLPGCAERWNSGASFKCTV 329
Cdd:cd04986   4 LSLQRPALEDLLLGSNASLTCTLSGLKDPEGATFTWEPSGGKEAIQGPPERDSCGCYSVSSVLPGCAEPWNSGDTFSCTV 83

                        90
                ....*....|...
gi 66794516 330 THPES-DTLTGTI 341
Cdd:cd04986  84 THPESkGTLTATI 96

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        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66794516 137 PTIYPLTFPQALSSDPVIIGCLIHDYFPSgTMNVTWGKSGKDITTVNFPPALASGGRYTMSSQLTLPAVECPEGESVKCS 216
Cdd:cd21818   2 PTVFPLSLCPSLSSDPVVIGCLVQGFFPE-PVNVTWNYSGKGGTARNFPAMLASGGRYTQSSQLTLPADQCPEGEAYKCS 80

                        90
                ....*....|....*
gi 66794516 217 VQHDsNPVQELNVNC 231
Cdd:cd21818  81 VQHY-SPSQDLNVPC 94

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66794516 250 LSLQRPALEDLLLGSDASITCTLNGLRDPEGAVFTWEPSTGKDAVQKKAVQNSCGCYSVSSVLPGCAERWNSGASFKCTV 329
Cdd:cd04986   4 LSLQRPALEDLLLGSNASLTCTLSGLKDPEGATFTWEPSGGKEAIQGPPERDSCGCYSVSSVLPGCAEPWNSGDTFSCTV 83

                        90
                ....*....|...
gi 66794516 330 THPES-DTLTGTI 341
Cdd:cd04986  84 THPESkGTLTATI 96

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        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66794516 137 PTIYPLTFPQALSSDPVIIGCLIHDYFPSgTMNVTWGKSGKDITTVNFPPALASGGRYTMSSQLTLPAVECPEGESVKCS 216
Cdd:cd21818   2 PTVFPLSLCPSLSSDPVVIGCLVQGFFPE-PVNVTWNYSGKGGTARNFPAMLASGGRYTQSSQLTLPADQCPEGEAYKCS 80

                        90
                ....*....|....*
gi 66794516 217 VQHDsNPVQELNVNC 231
Cdd:cd21818  81 VQHY-SPSQDLNVPC 94

Immunoglobulin C1-set domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66794516   353 VHLLPPPSEELalNELVSLTCLVRAFNPKEVLVRWLHGNEELsPESYLVFEPLKEPGEgatTYLVTSVLRVSAEIWKQGD 432
Cdd:pfam07654   1 VYVFPPSPEEL--GKPNTLTCLVTGFYPPDITVTWLKNGQEV-TEGVKTTPPSPNSDW---TYQLSSYLTVTPSDWESGD 74

                          90
                  ....*....|.
gi 66794516   433 QYSCMVGHEAL 443
Cdd:pfam07654  75 EYTCRVEHEGL 85

Immunoglobulin C1-set domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66794516   139 IYPLTFPQALSSDPVIIGCLIHDYFPsGTMNVTWGKSGKDITT--VNFPPALASGGRYTMSSQLTLPAVECPEGESVKCS 216
Cdd:pfam07654   1 VYVFPPSPEELGKPNTLTCLVTGFYP-PDITVTWLKNGQEVTEgvKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTCR 79

                  ....*.
gi 66794516   217 VQHDSN 222
Cdd:pfam07654  80 VEHEGL 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 66794516    29 LVQPGGSLKLSCAASGFDFSK-DWMSWVRQAPGKGLEWIGEINPDSSTInyaPSLKDKFIISRENAKNTLYLQMSKVRSE 107
Cdd:pfam07686   7 TVALGGSVTLPCTYSSSMSEAsTSVYWYRQPPGKGPTFLIAYYSNGSEE---GVKKGRFSGRGDPSNGDGSLTIQNLTLS 83

                          90       100
                  ....*....|....*....|....*
gi 66794516   108 DTALYYCARFLA---YWGQGTSVTV 129
Cdd:pfam07686  84 DSGTYTCAVIPSgegVFGKGTRLTV 108

Immunoglobulin C-Type;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 66794516    264 SDASITCTLNGLRDPEGAVfTWEPStgkdavqkkavQNSCGCYSVSSVLPGCAERWNSGASFKCTVTHP 332
Cdd:smart00407  14 PDITVTWLRNGQEVTEGVS-TTDPL-----------KNSDGTYFLSSYLTVPASTWESGDVYTCQVTHE 70

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66794516 250 LSLQRPALEDLLLGSDASITCTLNGLRDPEGAVFTWEPSTGKDAVQKKAVQNSCGCYSVSSVLPGCAERWNSGASFKCTV 329
Cdd:cd04986   4 LSLQRPALEDLLLGSNASLTCTLSGLKDPEGATFTWEPSGGKEAIQGPPERDSCGCYSVSSVLPGCAEPWNSGDTFSCTV 83

                        90
                ....*....|...
gi 66794516 330 THPES-DTLTGTI 341
Cdd:cd04986  84 THPESkGTLTATI 96

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        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66794516 137 PTIYPLTFPQALSSDPVIIGCLIHDYFPSgTMNVTWGKSGKDITTVNFPPALASGGRYTMSSQLTLPAVECPEGESVKCS 216
Cdd:cd21818   2 PTVFPLSLCPSLSSDPVVIGCLVQGFFPE-PVNVTWNYSGKGGTARNFPAMLASGGRYTQSSQLTLPADQCPEGEAYKCS 80

                        90
                ....*....|....*
gi 66794516 217 VQHDsNPVQELNVNC 231
Cdd:cd21818  81 VQHY-SPSQDLNVPC 94

Immunoglobulin V-Type;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66794516     35 SLKLSCAASGFDFSKDWMSWVRQAPGKGLEWIGEINPDSSTInYAPSLKDKFIISRENAKNTLYLQMSKVRSEDTALYYC 114
Cdd:smart00406   1 SVTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIGSNGSSY-YQESYKGRFTISKDTSKNDVSLTISNLRVEDTGTYYC 79

                   ..
gi 66794516    115 AR 116
Cdd:smart00406  80 AV 81

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 66794516  29 LVQPGGSLKLSCAASGFdFSKDWMSWVRQAPGKGLEWIGEINPDSSTINyaPSLKDKFIISReNAKNTLYLQMSKVRSED 108
Cdd:cd00099   9 SVQEGESVTLSCEVSSS-FSSTYIYWYRQKPGQGPEFLIYLSSSKGKTK--GGVPGRFSGSR-DGTSSFSLTISNLQPED 84

                        90       100
                ....*....|....*....|....*..
gi 66794516 109 TALYYCARFLA------YWGQGTSVTV 129
Cdd:cd00099  85 SGTYYCAVSESggtdklTFGSGTRLTV 111

Immunoglobulin C1-set domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66794516   139 IYPLTFPQALSSDPVIIGCLIHDYFPsGTMNVTWGKSGKDITT--VNFPPALASGGRYTMSSQLTLPAVECPEGESVKCS 216
Cdd:pfam07654   1 VYVFPPSPEELGKPNTLTCLVTGFYP-PDITVTWLKNGQEVTEgvKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTCR 79

                  ....*.
gi 66794516   217 VQHDSN 222
Cdd:pfam07654  80 VEHEGL 85

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66794516 137 PTIYPLTFPQALSSDPVIIGCLIHDYFPSgTMNVTWGKSGKDITT--VNFPPALaSGGRYTMSSQLTLPAVECPEGESVK 214
Cdd:cd21819   2 PTLFPLVSCGSSTSDPVTVGCLATDFLPD-SITFSWTDDNNSLTTgvKTYPSVL-TGGTYTASSQLQVPESEWKSKENFY 79

                        90
                ....*....|.
gi 66794516 215 CSVQHDSNPVQ 225
Cdd:cd21819  80 CKVEHPGGNKE 90

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 66794516 350 PPQVHLLPPPSEELALNELVSLTCLVRAFNPKEVLVRWLHGNEELSPESYLVFEPLKEPgeGATTYLVTSVLRVSAEIWK 429
Cdd:cd16093   1 PPTVSLHAPSREEFLGNRTATFVCLATGFSPKTISFKWLRNGKEVTSSTGAVVEEPKED--GKTLYSATSFLTITESEWK 78

                        90
                ....*....|....
gi 66794516 430 QGDQYSCMVGHEAL 443
Cdd:cd16093  79 SQTEFTCEFKHKGE 92

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 66794516  31 QPGGSLKLSCAASGFDFSKDWMSWVRQAPGKGLEWIGEINPDSSTINYAPSLKDKFIISRENAKNTLYLQMSKVRSEDTA 110
Cdd:cd04982  11 EESKSVTISCKVSGIDFSTTYIHWYRQKPGQALERLLYVSSTSAVRKDSGKTKNKFEARKDVGKSTSTLTITNLEKEDSA 90

                        90       100
                ....*....|....*....|....*..
gi 66794516 111 LYYCARFLA---YW----GQGTSVTVS 130
Cdd:cd04982  91 TYYCAYWESgsgYYikvfGSGTKLIVT 117

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 66794516 254 RPALEDLLLGSDASITCTLNGLRDPEGAVFTWEPSTGKD--AVQKKAVQNSCGCYSVSSVLPGCAERWNSGASFKCTVTH 331
Cdd:cd07696   7 PPSPKDLFLTKSAKVTCLVVDLTSIEEVNVTWSREDGNEvlASTTNPEKHYNATLSVVSTLTVCADDWDNGKTFKCKVTH 86

                .
gi 66794516 332 P 332
Cdd:cd07696  87 P 87

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66794516     25 SGGGLVQPGGSLKLSCAASGFdfSKDWMSWVRQapgkGLEWIGEinpdsstinyapslKDKFIISRENakNTLYLQMSKV 104
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGS--PPPEVTWYKQ----GGKLLAE--------------SGRFSVSRSG--STSTLTISNV 58

                           90       100
                   ....*....|....*....|....*..
gi 66794516    105 RSEDTALYYCARFLAYWG--QGTSVTV 129
Cdd:smart00410  59 TPEDSGTYTCAATNSSGSasSGTTLTV 85

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66794516 351 PQVHLLPPPSEELALNELVSLTCLVRAFNPKEVLVRWL-HGNEELSPESYLVfePLKEPGEgatTYLVTSVLRVSAEIWK 429
Cdd:cd05847   1 PTVQILHSSCASTLTSETIQLLCLISGYTPSTIEVEWLvDGQVATLSAASTA--PQKEEGG---TFSTTSKLNVTQEDWK 75

                        90
                ....*....|....
gi 66794516 430 QGDQYSCMVGHEAL 443
Cdd:cd05847  76 SGKTYTCKVTHQGT 89

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66794516 250 LSLQRPALEDLLlGSDASITCTLNGLRdPEGAVFTWEP---STGKDAVQKKAVQNSCGCYSVSSVLPGCAERWNSGASFK 326
Cdd:cd00098   2 VTLLPPSPEEKG-GGKVTLVCLVSGFY-PKDITVTWLKngvPLTSGVSTSSPVEPNDGTYSVTSSLTVPPSDWDEGATYT 79

                        90
                ....*....|
gi 66794516 327 CTVTHPESDT 336
Cdd:cd00098  80 CVVTHESLKS 89

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 66794516  30 VQPGGSLKLSCAASGFDFSKDWMSWVRQAPGKGLEWIgeINPDSSTINYAPslkDKFiiSRENAKNTLYLQMSKVRSEDT 109
Cdd:cd04984  10 VSPGETVTITCTGSSGNISGNYVNWYQQKPGSAPRYL--IYEDKHRPSGIP---DRF--SGSKSGNTASLTISGAQTEDE 82

                        90       100
                ....*....|....*....|...
gi 66794516 110 ALYYCA---RFLAYWGQGTSVTV 129
Cdd:cd04984  83 ADYYCQvwdSNSYVFGGGTKLTV 105

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 66794516    29 LVQPGGSLKLSCAASGFDFSK-DWMSWVRQAPGKGLEWIGEINPDSSTInyaPSLKDKFIISRENAKNTLYLQMSKVRSE 107
Cdd:pfam07686   7 TVALGGSVTLPCTYSSSMSEAsTSVYWYRQPPGKGPTFLIAYYSNGSEE---GVKKGRFSGRGDPSNGDGSLTIQNLTLS 83

                          90       100
                  ....*....|....*....|....*
gi 66794516   108 DTALYYCARFLA---YWGQGTSVTV 129
Cdd:pfam07686  84 DSGTYTCAVIPSgegVFGKGTRLTV 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 66794516 250 LSLQRPALEDLLLGSDASITCTLNGLRdPEGAVFTW-----EPSTGKDAVQKKAVQNSCGCYSVSSVLPGCAERWNSGAS 324
Cdd:cd16093   4 VSLHAPSREEFLGNRTATFVCLATGFS-PKTISFKWlrngkEVTSSTGAVVEEPKEDGKTLYSATSFLTITESEWKSQTE 82

                        90
                ....*....|
gi 66794516 325 FKCTVTHPES 334
Cdd:cd16093  83 FTCEFKHKGE 92

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 66794516  30 VQPGGSLKLSCaasgfDFSKDWMS---WVRQAPGKGLEWIGEINPDSSTINyapslKDKFIISRENAKNTLYLQMSKVRS 106
Cdd:cd04983  10 VQEGENVTLNC-----NYSTSTFYylfWYRQYPGQGPQFLIYISSDSGNKK-----KGRFSATLDKSRKSSSLHISAAQL 79

                        90       100
                ....*....|....*....|....*....
gi 66794516 107 EDTALYYCARFLAYW------GQGTSVTV 129
Cdd:cd04983  80 SDSAVYFCALSESGGtgkltfGKGTRLTV 108

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 66794516 350 PPQVHLLPPPSEElalnELVSLTCLVRAFNPKEVLVRWLHGNEELSPESYLVfEPLkeP-GEGatTYLVTSVLRVSAEIW 428
Cdd:cd07698   2 PPKVHVTHHPRSD----GESTLRCWALGFYPAEITLTWQRDGEDQTQDMELV-ETR--PnGDG--TFQKWAAVVVPSGEE 72

                        90
                ....*....|....*..
gi 66794516 429 KQgdqYSCMVGHEALPM 445
Cdd:cd07698  73 QR---YTCHVQHEGLPE 86

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 66794516 350 PPQVHLLPPPseelALN--ELVSLTCLVRAFNPKEVLVRWLHGNEELSPESYlvfEPLKEPGEGATTYLVTSVLRVSAei 427
Cdd:cd21002   3 PPSVRVAPTT----PFNtrEPVMLACHVWGFYPADVTITWLKNGDPVAPHSS---APKTAQPNGDWTYQTQVTLAVTP-- 73

                        90
                ....*....|....*..
gi 66794516 428 wKQGDQYSCMVGHEALP 444
Cdd:cd21002  74 -SPGDTYTCSVQHASLP 89

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66794516 250 LSLQRPALEDLLLGSdASITCTLNGLRdPEGAVFTW--EPSTGKDAVQK-KAVQNSCGCYSVSSVLPGCAERWNSGASFK 326
Cdd:cd07699   4 VTIFPPSSEELSSGK-ATLVCLINKFY-PGFATVTWkvDGSTVSSGVTTsKTEQQSDNTYSMSSYLTLSSSDWNKHKVYT 81

                        90
                ....*....|....*..
gi 66794516 327 CTVTHPesdTLTGTIAK 343
Cdd:cd07699  82 CEVTHE---GLSSTITK 95

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        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66794516 359 PSEELALNELVSLTCLVRAFNPKEVLVRWLHGNEELSpeSYLVFEPLKEPGEgaTTYLVTSVLRVSAEiwkQGDQYSCMV 438
Cdd:cd21001  10 PSRTEALNHHNLLVCSVTDFYPGQIKVRWFRNDQEET--AGVVSTPLIRNGD--WTFQILVMLEMTPQ---RGDVYTCHV 82

                ....*
gi 66794516 439 GHEAL 443
Cdd:cd21001  83 EHPSL 87

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 66794516  30 VQPGGSLKLSCAASGfDFSKDWMSWVRQAPGKglewigeinPDSSTINYAPSLK----DKFIISRENAKNTlyLQMSKVR 105
Cdd:cd04980  12 VSPGERVTISCKASQ-SISSNYLAWYQQKPGQ---------APKLLIYYASTLHsgvpSRFSGSGSGTDFT--LTISSVE 79

                        90       100
                ....*....|....*....|....*..
gi 66794516 106 SEDTALYYCAR---FLAYWGQGTSVTV 129
Cdd:cd04980  80 PEDAAVYYCQQgytFPYTFGGGTKLEI 106