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Conserved domains on  [gi|16902046|gb|AAL27653|]
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anti-HLA class II antibody F3.3 kappa light chain variable region [Mus musculus]

Protein Classification

immunoglobulin domain-containing family protein( domain architecture ID 34076)

immunoglobulin (Ig) domain-containing family protein is a member of a large superfamily containing cell surface antigen receptors, co-receptors and co-stimulatory molecules of the immune system, molecules involved in antigen presentation to lymphocytes, cell adhesion molecules, certain cytokine receptors and intracellular muscle proteins; immunoglobulin domains are typically divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
4-107 5.30e-44

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.


The actual alignment was detected with superfamily member cd04980:

Pssm-ID: 448366  Cd Length: 106  Bit Score: 138.68  E-value: 5.30e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16902046   4 IELTQSPAIMSVFPGEKVTMTCSASSIVR--YMYWFQQKPGSSPRLLIYDTSSLSSGVPVRFSGSGSGTSYSLTISRMEA 81
Cdd:cd04980   1 IVMTQSPASLSVSPGERVTISCKASQSISsnYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISSVEP 80
                        90       100
                ....*....|....*....|....*.
gi 16902046  82 VDAATYFCQQWSSYPLTFGGGTKLEI 107
Cdd:cd04980  81 EDAAVYYCQQGYTFPYTFGGGTKLEI 106
 
Name Accession Description Interval E-value
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
4-107 5.30e-44

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.


Pssm-ID: 409369  Cd Length: 106  Bit Score: 138.68  E-value: 5.30e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16902046   4 IELTQSPAIMSVFPGEKVTMTCSASSIVR--YMYWFQQKPGSSPRLLIYDTSSLSSGVPVRFSGSGSGTSYSLTISRMEA 81
Cdd:cd04980   1 IVMTQSPASLSVSPGERVTISCKASQSISsnYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISSVEP 80
                        90       100
                ....*....|....*....|....*.
gi 16902046  82 VDAATYFCQQWSSYPLTFGGGTKLEI 107
Cdd:cd04980  81 EDAAVYYCQQGYTFPYTFGGGTKLEI 106
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
8-107 1.42e-13

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


Pssm-ID: 429596  Cd Length: 109  Bit Score: 61.32  E-value: 1.42e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16902046     8 QSPAIMSVFPGEKVTMTCSASSIVR----YMYWFQQKPGSSPRLLIYDTSSLS----SGVPVRFSGSGSGTSYSLTISRM 79
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYSSSMSeastSVYWYRQPPGKGPTFLIAYYSNGSeegvKKGRFSGRGDPSNGDGSLTIQNL 80
                          90       100
                  ....*....|....*....|....*...
gi 16902046    80 EAVDAATYFCQQWSSYPLTFGGGTKLEI 107
Cdd:pfam07686  81 TLSDSGTYTCAVIPSGEGVFGKGTRLTV 108
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
10-107 1.28e-11

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: 55.59  E-value: 1.28e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16902046     10 PAIMSVFPGEKVTMTCSASS-IVRYMYWFQQKPgsspRLLIYDTsslssgvpvRFSGSGSGTSYSLTISRMEAVDAATYF 88
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGsPPPEVTWYKQGG----KLLAESG---------RFSVSRSGSTSTLTISNVTPEDSGTYT 67
                           90
                   ....*....|....*....
gi 16902046     89 CQQWSSYPLTFgGGTKLEI 107
Cdd:smart00410  68 CAATNSSGSAS-SGTTLTV 85
 
Name Accession Description Interval E-value
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
4-107 5.30e-44

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.


Pssm-ID: 409369  Cd Length: 106  Bit Score: 138.68  E-value: 5.30e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16902046   4 IELTQSPAIMSVFPGEKVTMTCSASSIVR--YMYWFQQKPGSSPRLLIYDTSSLSSGVPVRFSGSGSGTSYSLTISRMEA 81
Cdd:cd04980   1 IVMTQSPASLSVSPGERVTISCKASQSISsnYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISSVEP 80
                        90       100
                ....*....|....*....|....*.
gi 16902046  82 VDAATYFCQQWSSYPLTFGGGTKLEI 107
Cdd:cd04980  81 EDAAVYYCQQGYTFPYTFGGGTKLEI 106
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
5-105 1.64e-31

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.


Pssm-ID: 409373  Cd Length: 105  Bit Score: 106.78  E-value: 1.64e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16902046   5 ELTQSPAImSVFPGEKVTMTCSASSIVR---YMYWFQQKPGSSPRLLIYDTSSLSSGVPVRFSGSGSGTSYSLTISRMEA 81
Cdd:cd04984   1 VLTQPSSL-SVSPGETVTITCTGSSGNIsgnYVNWYQQKPGSAPRYLIYEDKHRPSGIPDRFSGSKSGNTASLTISGAQT 79
                        90       100
                ....*....|....*....|....
gi 16902046  82 VDAATYFCQQWSSYPLTFGGGTKL 105
Cdd:cd04984  80 EDEADYYCQVWDSNSYVFGGGTKL 103
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
6-107 6.11e-29

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: 100.49  E-value: 6.11e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16902046   6 LTQSPAIMSVFPGEKVTMTCSASS--IVRYMYWFQQKPGSSPRLLIY---DTSSLSSGVPVRFSGSGSGTSY-SLTISRM 79
Cdd:cd00099   1 VTQSPRSLSVQEGESVTLSCEVSSsfSSTYIYWYRQKPGQGPEFLIYlssSKGKTKGGVPGRFSGSRDGTSSfSLTISNL 80
                        90       100       110
                ....*....|....*....|....*....|.
gi 16902046  80 EAVDAATYFCQQWSS---YPLTFGGGTKLEI 107
Cdd:cd00099  81 QPEDSGTYYCAVSESggtDKLTFGSGTRLTV 111
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
6-105 8.24e-21

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: 80.02  E-value: 8.24e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16902046   6 LTQSPAIMSVFPGEKVTMTCSASSIVRYMYWFQQKPGSSPRLLIYDTSSLS---SGVPV-RFSGS-GSGTSYSLTISRME 80
Cdd:cd05899   1 VTQSPRYLIKRRGQSVTLRCSQKSGHDNMYWYRQDPGKGLQLLFYSYGGGLneeGDLPGdRFSASrPSLTRSSLTIKSAE 80
                        90       100
                ....*....|....*....|....*...
gi 16902046  81 AVDAATYFC---QQWSSYPLTFGGGTKL 105
Cdd:cd05899  81 PEDSAVYLCassLGGGADEAYFGPGTRL 108
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
7-108 3.97e-17

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: 70.38  E-value: 3.97e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16902046   7 TQSPAIMSVFPGEKVTMTCSASSIV-RYMYWFQQKPGSSPRLLIYDTSSLSSGVPVRFSGS--GSGTSYSLTISRMEAVD 83
Cdd:cd04983   2 TQSPQSLSVQEGENVTLNCNYSTSTfYYLFWYRQYPGQGPQFLIYISSDSGNKKKGRFSATldKSRKSSSLHISAAQLSD 81
                        90       100
                ....*....|....*....|....*...
gi 16902046  84 AATYFC---QQWSSYPLTFGGGTKLEIK 108
Cdd:cd04983  82 SAVYFCalsESGGTGKLTFGKGTRLTVE 109
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
8-107 1.42e-13

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


Pssm-ID: 429596  Cd Length: 109  Bit Score: 61.32  E-value: 1.42e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16902046     8 QSPAIMSVFPGEKVTMTCSASSIVR----YMYWFQQKPGSSPRLLIYDTSSLS----SGVPVRFSGSGSGTSYSLTISRM 79
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYSSSMSeastSVYWYRQPPGKGPTFLIAYYSNGSeegvKKGRFSGRGDPSNGDGSLTIQNL 80
                          90       100
                  ....*....|....*....|....*...
gi 16902046    80 EAVDAATYFCQQWSSYPLTFGGGTKLEI 107
Cdd:pfam07686  81 TLSDSGTYTCAVIPSGEGVFGKGTRLTV 108
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
10-107 1.28e-11

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: 55.59  E-value: 1.28e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16902046     10 PAIMSVFPGEKVTMTCSASS-IVRYMYWFQQKPgsspRLLIYDTsslssgvpvRFSGSGSGTSYSLTISRMEAVDAATYF 88
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGsPPPEVTWYKQGG----KLLAESG---------RFSVSRSGSTSTLTISNVTPEDSGTYT 67
                           90
                   ....*....|....*....
gi 16902046     89 CQQWSSYPLTFgGGTKLEI 107
Cdd:smart00410  68 CAATNSSGSAS-SGTTLTV 85
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
6-105 1.53e-11

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.


Pssm-ID: 409371  Cd Length: 117  Bit Score: 56.22  E-value: 1.53e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16902046   6 LTQSPAIMSVFPGEKVTMTCSASSIV---RYMYWFQQKPGSSPRLLIYDTSS-----LSSGVPVRFSG--SGSGTSYSLT 75
Cdd:cd04982   1 LEQPQLSITREESKSVTISCKVSGIDfstTYIHWYRQKPGQALERLLYVSSTsavrkDSGKTKNKFEArkDVGKSTSTLT 80
                        90       100       110
                ....*....|....*....|....*....|....
gi 16902046  76 ISRMEAVDAATYFCQQWSSYPLT----FGGGTKL 105
Cdd:cd04982  81 ITNLEKEDSATYYCAYWESGSGYyikvFGSGTKL 114
IgV_TCR_delta cd07706
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here ...
5-107 8.89e-11

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: 54.06  E-value: 8.89e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16902046   5 ELTQSPAIMSVFPGEKVTMTC--SASSIVRYMYWFQQKPGSSPRLLIYDTSSLSSGVPVRFSG--SGSGTSYSLTISRME 80
Cdd:cd07706   1 KVTQAQPDVSVQVGEEVTLNCryETSWTNYYLFWYKQLPSGEMTFLIRQDSSEQNAKSGRYSVnfQKAQKSISLTISALQ 80
                        90       100       110
                ....*....|....*....|....*....|
gi 16902046  81 AVDAATYFCQQWSSYP---LTFGGGTKLEI 107
Cdd:cd07706  81 LEDSAKYFCALSLPYDtdkLIFGKGTRLTV 110
IGv smart00406
Immunoglobulin V-Type;
21-91 1.23e-09

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 50.46  E-value: 1.23e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16902046     21 VTMTCSAS--SIVRY-MYWFQQKPGSSPRLLIYDTSS----LSSGVPVRFSGSGSGTSY--SLTISRMEAVDAATYFCQQ 91
Cdd:smart00406   2 VTLSCKFSgsTFSSYyVSWVRQPPGKGLEWLGYIGSNgssyYQESYKGRFTISKDTSKNdvSLTISNLRVEDTGTYYCAV 81
IgV_CD8_beta cd07700
Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The ...
6-107 1.82e-05

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


Pssm-ID: 409497  Cd Length: 116  Bit Score: 40.51  E-value: 1.82e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16902046   6 LTQSPAIMSVFPGEKVTMTCSASSIVRYM--YWFQQKPGSSPR-----LLIYDtsslSSGVPV----------RFSGSGS 68
Cdd:cd07700   1 LLQTPGSLLVQTNQTVKMSCEAKTSPKNTriYWLRQRQAPSKDshfefLASWD----PSKGIVygegvdqeklIILSDSD 76
                        90       100       110
                ....*....|....*....|....*....|....*....
gi 16902046  69 GTSYSLTISRMEAVDAATYFCQQWSSYPLTFGGGTKLEI 107
Cdd:cd07700  77 SSRYILSLMSVKPEDSGTYFCMTVGSPELIFGTGTKLSV 115
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
5-90 1.36e-04

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 433584 [Multi-domain]  Cd Length: 75  Bit Score: 37.18  E-value: 1.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16902046     5 ELTQSPAIMSVFPGEKVTMTCSASSIVRYMYW--FQQKPGSSPRLLIYDTSSLssgvpvrfsgsgsgtsysLTISRMEAV 82
Cdd:pfam13927   3 VITVSPSSVVVVEGETVTLTCEASGSPPPTITwyKNGGKLSSGRTSLVGGNGT------------------LTISNVTRE 64

                  ....*...
gi 16902046    83 DAATYFCQ 90
Cdd:pfam13927  65 DSGTYTCT 72
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
5-89 3.90e-04

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.


Pssm-ID: 409370 [Multi-domain]  Cd Length: 118  Bit Score: 36.90  E-value: 3.90e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16902046   5 ELTQSPAiMSVFPGEKVTMTCSASSIV---RYMYWFQQKPGSSP---RLLIYDTSSLSSGVPVR----FSGSGSGTSYSL 74
Cdd:cd04981   1 QLQESGP-GLVKPGQSLKLSCKASGFTftsYGMGWVRQAPGKGLewiGLIYPGGGDTYYADSFKgrftITRDTSKSTAYL 79
                        90
                ....*....|....*
gi 16902046  75 TISRMEAVDAATYFC 89
Cdd:cd04981  80 QLNSLTSEDTAVYYC 94
IgV_SIRP cd16097
Immunoglobulin (Ig)-like variable (V) domain of the Signal-Regulatory Protein (SIRP); The ...
5-108 4.31e-03

Immunoglobulin (Ig)-like variable (V) domain of the Signal-Regulatory Protein (SIRP); The members here are composed of the immunoglobulin (Ig)-like domain of the Signal-Regulatory Protein (SIRP). The SIRPs belong to the "paired receptors" class of membrane proteins that comprise several genes coding for proteins with similar extracellular regions, but very different transmembrane/cytoplasmic regions with different (activating or inhibitory) signaling potentials. They are commonly on NK cells, but are also on many myeloid cells. Their extracellular region contains three immunoglobulin superfamily domains, a single V-set, and two C1-set IgSF domains. Their cytoplasmic tails that contain either ITIMs or transmembrane regions have positively charged residues that allow an association with adaptor proteins, such as DAP12/KARAP, containing ITAMs. There are 3 distinct SIRP members: alpha, beta, and gamma. SIRP alpha (also known as CD172a or SRC homology 2 domain-containing protein tyrosine phosphatase substrate 1/Shps-1) is a membrane receptor that interacts with a ligand CD47 expressed on many cells and gives an inhibitory signal through immunoreceptor tyrosine-based inhibition motifs in the cytoplasmic region that interact with phosphatases SHP-1 and SHP-2. SIRP beta has a short cytoplasmic region and associates with a transmembrane adapter protein DAP12 containing immunoreceptor tyrosine-based activation motifs to give an activating signal. SIRP gamma contains a very short cytoplasmic region lacking obvious signaling motifs, but also binds CD47 with much less affinity. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409516  Cd Length: 111  Bit Score: 34.07  E-value: 4.31e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16902046   5 ELTQSPAIMSVFPGEKVTMTCSASSI--VRYMYWFQqkpGSSP-RLLIYDTSS--LSSGVPVRFSGSGSGTSYSLTISRM 79
Cdd:cd16097   1 QVIQPEKSVSVAAGESATLHCTVTSLipVGPIQWFR---GAGPgRELIYNQKEghFPRVTTVSDLTKRNNMDFSIRISNI 77
                        90       100       110
                ....*....|....*....|....*....|....
gi 16902046  80 EAVDAATYFC---QQWSSYPLTF--GGGTKLEIK 108
Cdd:cd16097  78 TPADAGTYYCvkfRKGSPDDVEFksGAGTELSVR 111
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
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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