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Conserved domains on  [gi|20150828|pdb|1KJ2|B]
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Chain B, KB5-C20 T-Cell receptor beta-chain

Protein Classification

T-cell receptor beta chain V region( domain architecture ID 10147293)

T-cell receptor beta chain V (variable) region participates in the antigen recognition of an alpha-beta T cell antigen-specific receptor essential to the immune response; it is present on the cell surface of T lymphocytes to recognize peptide-major histocompatibility (pMH) complexes displayed by antigen presenting cells (APC), a prerequisite for efficient T cell adaptive immunity against pathogens

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 4-116 9.72e-42

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.


:

Pssm-ID: 409480  Cd Length: 110  Bit Score: 133.18  E-value: 9.72e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KJ2_B        4 LEQNPRWRLVPRGQAVNLRCILKnSQYPWMSWYQQDLQKQLQWLFTLRSPGDKEVKSLPGADYLATRVTDTELRLQVANM 83
Cdd:cd05899   1 VTQSPRYLIKRRGQSVTLRCSQK-SGHDNMYWYRQDPGKGLQLLFYSYGGGLNEEGDLPGDRFSASRPSLTRSSLTIKSA 79

                        90       100       110
                ....*....|....*....|....*....|....*
1KJ2_B       84 S--QGRTLYCTCSAAPDwgasAETLYFGSGTRLTV 116
Cdd:cd05899  80 EpeDSAVYLCASSLGGG----ADEAYFGPGTRLTV 110
 
Name Accession Description Interval E-value
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 4-116 9.72e-42

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.


Pssm-ID: 409480  Cd Length: 110  Bit Score: 133.18  E-value: 9.72e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KJ2_B        4 LEQNPRWRLVPRGQAVNLRCILKnSQYPWMSWYQQDLQKQLQWLFTLRSPGDKEVKSLPGADYLATRVTDTELRLQVANM 83
Cdd:cd05899   1 VTQSPRYLIKRRGQSVTLRCSQK-SGHDNMYWYRQDPGKGLQLLFYSYGGGLNEEGDLPGDRFSASRPSLTRSSLTIKSA 79

                        90       100       110
                ....*....|....*....|....*....|....*
1KJ2_B       84 S--QGRTLYCTCSAAPDwgasAETLYFGSGTRLTV 116
Cdd:cd05899  80 EpeDSAVYLCASSLGGG----ADEAYFGPGTRLTV 110
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 6-117 4.28e-16

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


Pssm-ID: 462230  Cd Length: 109  Bit Score: 68.25  E-value: 4.28e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KJ2_B          6 QNPRWRLVPRGQAVNLRCILKNS---QYPWMSWYQQDLQKQLQWLFTLRSPGDKEVKsLPGADYLA--TRVTDTELRLQV 80
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYSSSmseASTSVYWYRQPPGKGPTFLIAYYSNGSEEGV-KKGRFSGRgdPSNGDGSLTIQN 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
1KJ2_B         81 ANMSQGRTLYCTCsaapdwgASAETLYFGSGTRLTVL 117
Cdd:pfam07686  80 LTLSDSGTYTCAV-------IPSGEGVFGKGTRLTVL 109
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 8-42 2.94e-04

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


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 36.71  E-value: 2.94e-04
                           10        20        30
                   ....*....|....*....|....*....|....*
1KJ2_B           8 PRWRLVPRGQAVNLRCILKNSQYPWMSWYQQDLQK 42
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGSPPPEVTWYKQGGKL 35
 
Name Accession Description Interval E-value
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 4-116 9.72e-42

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.


Pssm-ID: 409480  Cd Length: 110  Bit Score: 133.18  E-value: 9.72e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KJ2_B        4 LEQNPRWRLVPRGQAVNLRCILKnSQYPWMSWYQQDLQKQLQWLFTLRSPGDKEVKSLPGADYLATRVTDTELRLQVANM 83
Cdd:cd05899   1 VTQSPRYLIKRRGQSVTLRCSQK-SGHDNMYWYRQDPGKGLQLLFYSYGGGLNEEGDLPGDRFSASRPSLTRSSLTIKSA 79

                        90       100       110
                ....*....|....*....|....*....|....*
1KJ2_B       84 S--QGRTLYCTCSAAPDwgasAETLYFGSGTRLTV 116
Cdd:cd05899  80 EpeDSAVYLCASSLGGG----ADEAYFGPGTRLTV 110
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 4-116 2.02e-21

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.


Pssm-ID: 409355 [Multi-domain]  Cd Length: 111  Bit Score: 81.61  E-value: 2.02e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KJ2_B        4 LEQNPRWRLVPRGQAVNLRCILKNS-QYPWMSWYQQDLQKQLQWLFTLRSPGDKeVKSLPGADYLATRVTDTELRLQVAN 82
Cdd:cd00099   1 VTQSPRSLSVQEGESVTLSCEVSSSfSSTYIYWYRQKPGQGPEFLIYLSSSKGK-TKGGVPGRFSGSRDGTSSFSLTISN 79

                        90       100       110
                ....*....|....*....|....*....|....*.
1KJ2_B       83 M--SQGRTLYCTCSAAPdwgaSAETLYFGSGTRLTV 116
Cdd:cd00099  80 LqpEDSGTYYCAVSESG----GTDKLTFGSGTRLTV 111
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 6-117 4.28e-16

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


Pssm-ID: 462230  Cd Length: 109  Bit Score: 68.25  E-value: 4.28e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KJ2_B          6 QNPRWRLVPRGQAVNLRCILKNS---QYPWMSWYQQDLQKQLQWLFTLRSPGDKEVKsLPGADYLA--TRVTDTELRLQV 80
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYSSSmseASTSVYWYRQPPGKGPTFLIAYYSNGSEEGV-KKGRFSGRgdPSNGDGSLTIQN 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
1KJ2_B         81 ANMSQGRTLYCTCsaapdwgASAETLYFGSGTRLTVL 117
Cdd:pfam07686  80 LTLSDSGTYTCAV-------IPSGEGVFGKGTRLTVL 109
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 5-116 2.60e-09

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.


Pssm-ID: 409372 [Multi-domain]  Cd Length: 109  Bit Score: 50.73  E-value: 2.60e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KJ2_B        5 EQNPRWRLVPRGQAVNLRCILKNSQYPWMSWYQQDLQKQLQWLFTLRSPGDKEVKSLPGADYLATRvTDTELRLQVANMS 84
Cdd:cd04983   2 TQSPQSLSVQEGENVTLNCNYSTSTFYYLFWYRQYPGQGPQFLIYISSDSGNKKKGRFSATLDKSR-KSSSLHISAAQLS 80

                        90       100       110
                ....*....|....*....|....*....|..
1KJ2_B       85 QGRTLYCtcsAAPDWGaSAETLYFGSGTRLTV 116
Cdd:cd04983  81 DSAVYFC---ALSESG-GTGKLTFGKGTRLTV 108
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 8-42 2.94e-04

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


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 36.71  E-value: 2.94e-04
                           10        20        30
                   ....*....|....*....|....*....|....*
1KJ2_B           8 PRWRLVPRGQAVNLRCILKNSQYPWMSWYQQDLQK 42
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGSPPPEVTWYKQGGKL 35
IgV_H_TCR_mu cd16095
T-cell receptor Mu, Heavy chain, variable (V) domain; The members here are composed of the ...
 14-116 3.66e-04

T-cell receptor Mu, Heavy chain, variable (V) domain; The members here are composed of the immunoglobulin (Ig) heavy chain (H), variable (V) domain of the T-cell receptor Mu. 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. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409514  Cd Length: 115  Bit Score: 37.16  E-value: 3.66e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KJ2_B       14 PRGQAVNLRC-----ILKNSQypwMSWYQQDLQKQLQWLFTLRSpgdkeVKSLPGADYLATRVTDTE--LRLQVANMSQG 86
Cdd:cd16095  13 PAGKTLSLKCqtsgfQFNTSQ---LSWYLWVPGHAPLWLTSLDH-----ISTKVSEDRITSSREDTNsqIFLQIKGLGLR 84

                        90       100       110
                ....*....|....*....|....*....|
1KJ2_B       87 RTLYCTCSAAPDWGASAETLYFGSGTRLTV 116
Cdd:cd16095  85 DSGQYHCARRVGYGDDTDKLIFGPGTDVIV 114
IgV_TCR_delta cd07706
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here ...
 13-116 3.87e-03

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.


Pssm-ID: 409503  Cd Length: 112  Bit Score: 34.42  E-value: 3.87e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1KJ2_B       13 VPRGQAVNLRCILKNS-QYPWMSWYQQDLQKQLQWLFTLRSPGDKEVKSLPGADYLATR----VTDTELRLQvanmsQGR 87
Cdd:cd07706  11 VQVGEEVTLNCRYETSwTNYYLFWYKQLPSGEMTFLIRQDSSEQNAKSGRYSVNFQKAQksisLTISALQLE-----DSA 85

                        90       100
                ....*....|....*....|....*....
1KJ2_B       88 TLYCTCSAAPDwgasAETLYFGSGTRLTV 116
Cdd:cd07706  86 KYFCALSLPYD----TDKLIFGKGTRLTV 110
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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