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Conserved domains on  [gi|56972362|gb|AAH88126|]
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CD8a molecule [Rattus norvegicus]

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 ...
 28-137 1.08e-40

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 cd05720:

Pssm-ID: 472250  Cd Length: 110  Bit Score: 135.30  E-value: 1.08e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56972362  28 LQLSPKKVDAEIGQEVKLTCEVLRDTSQGCSWLFRNSSSeLLQPTFIIYVS-SSRSKLNDILDPNLFSARKENNKYILTL 106
Cdd:cd05720   1 FRMSPRKRDAQLGQKVELVCEVLNSVPQGCSWLFQPRGS-APQPTFLLYLSsSNKTKWAEGLDSKRFSGSRSGSSYVLTL 79

                        90       100       110
                ....*....|....*....|....*....|.
gi 56972362 107 SKFSTKNQGYYFCSITSNSVMYFSPLVPVFQ 137
Cdd:cd05720  80 KDFRKEDEGYYFCSVISNSVLYFSSFVPVFL 110
 
Name Accession Description Interval E-value
IgV_CD8_alpha cd05720
Immunoglobulin (Ig)-like variable (V) domain of Cluster of Differentiation (CD) 8 alpha chain; ...
 28-137 1.08e-40

Immunoglobulin (Ig)-like variable (V) domain of Cluster of Differentiation (CD) 8 alpha chain; The members here are composed of the immunoglobulin (Ig)-like variable domain of the Cluster of Differentiation (CD) 8 alpha. 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. The Ig domain of CD8 alpha binds to antibodies. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409385  Cd Length: 110  Bit Score: 135.30  E-value: 1.08e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56972362  28 LQLSPKKVDAEIGQEVKLTCEVLRDTSQGCSWLFRNSSSeLLQPTFIIYVS-SSRSKLNDILDPNLFSARKENNKYILTL 106
Cdd:cd05720   1 FRMSPRKRDAQLGQKVELVCEVLNSVPQGCSWLFQPRGS-APQPTFLLYLSsSNKTKWAEGLDSKRFSGSRSGSSYVLTL 79

                        90       100       110
                ....*....|....*....|....*....|.
gi 56972362 107 SKFSTKNQGYYFCSITSNSVMYFSPLVPVFQ 137
Cdd:cd05720  80 KDFRKEDEGYYFCSVISNSVLYFSSFVPVFL 110
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 31-135 1.14e-10

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: 57.08  E-value: 1.14e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56972362    31 SPKKVDAEIGQEVKLTCEVLR---DTSQGCSWLFRNSSSellQPTFIIYVSSSrsKLNDILDPNLFSARK--ENNKYILT 105
Cdd:pfam07686   2 TPREVTVALGGSVTLPCTYSSsmsEASTSVYWYRQPPGK---GPTFLIAYYSN--GSEEGVKKGRFSGRGdpSNGDGSLT 76

                          90       100       110
                  ....*....|....*....|....*....|
gi 56972362   106 LSKFSTKNQGYYFCSITSNSVMYFSPLVPV 135
Cdd:pfam07686  77 IQNLTLSDSGTYTCAVIPSGEGVFGKGTRL 106
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 32-131 1.69e-07

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: 47.50  E-value: 1.69e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56972362     32 PKKVDAEIGQEVKLTCEVLRDTSQGCSWLfrnsssellqptfiiyvsssRSKLNDILDPNLFSARKENNKYILTLSKFST 111
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGSPPPEVTWY--------------------KQGGKLLAESGRFSVSRSGSTSTLTISNVTP 60

                           90       100
                   ....*....|....*....|
gi 56972362    112 KNQGYYFCSITSNSVMYFSP 131
Cdd:smart00410  61 EDSGTYTCAATNSSGSASSG 80
 
Name Accession Description Interval E-value
IgV_CD8_alpha cd05720
Immunoglobulin (Ig)-like variable (V) domain of Cluster of Differentiation (CD) 8 alpha chain; ...
 28-137 1.08e-40

Immunoglobulin (Ig)-like variable (V) domain of Cluster of Differentiation (CD) 8 alpha chain; The members here are composed of the immunoglobulin (Ig)-like variable domain of the Cluster of Differentiation (CD) 8 alpha. 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. The Ig domain of CD8 alpha binds to antibodies. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409385  Cd Length: 110  Bit Score: 135.30  E-value: 1.08e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56972362  28 LQLSPKKVDAEIGQEVKLTCEVLRDTSQGCSWLFRNSSSeLLQPTFIIYVS-SSRSKLNDILDPNLFSARKENNKYILTL 106
Cdd:cd05720   1 FRMSPRKRDAQLGQKVELVCEVLNSVPQGCSWLFQPRGS-APQPTFLLYLSsSNKTKWAEGLDSKRFSGSRSGSSYVLTL 79

                        90       100       110
                ....*....|....*....|....*....|.
gi 56972362 107 SKFSTKNQGYYFCSITSNSVMYFSPLVPVFQ 137
Cdd:cd05720  80 KDFRKEDEGYYFCSVISNSVLYFSSFVPVFL 110
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 31-131 1.14e-12

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: 62.35  E-value: 1.14e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56972362  31 SPKKVDAEIGQEVKLTCEVL-RDTSQGCSWLFRNSSSellQPTFIIYVSSSRSKLNDiLDPNLFSA-RKENNKYILTLSK 108
Cdd:cd00099   4 SPRSLSVQEGESVTLSCEVSsSFSSTYIYWYRQKPGQ---GPEFLIYLSSSKGKTKG-GVPGRFSGsRDGTSSFSLTISN 79

                        90       100
                ....*....|....*....|....*.
gi 56972362 109 FSTKNQGYYFCSITSNS---VMYFSP 131
Cdd:cd00099  80 LQPEDSGTYYCAVSESGgtdKLTFGS 105
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 31-135 1.14e-10

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: 57.08  E-value: 1.14e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56972362    31 SPKKVDAEIGQEVKLTCEVLR---DTSQGCSWLFRNSSSellQPTFIIYVSSSrsKLNDILDPNLFSARK--ENNKYILT 105
Cdd:pfam07686   2 TPREVTVALGGSVTLPCTYSSsmsEASTSVYWYRQPPGK---GPTFLIAYYSN--GSEEGVKKGRFSGRGdpSNGDGSLT 76

                          90       100       110
                  ....*....|....*....|....*....|
gi 56972362   106 LSKFSTKNQGYYFCSITSNSVMYFSPLVPV 135
Cdd:pfam07686  77 IQNLTLSDSGTYTCAVIPSGEGVFGKGTRL 106
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 32-131 1.69e-07

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: 47.50  E-value: 1.69e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56972362     32 PKKVDAEIGQEVKLTCEVLRDTSQGCSWLfrnsssellqptfiiyvsssRSKLNDILDPNLFSARKENNKYILTLSKFST 111
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGSPPPEVTWY--------------------KQGGKLLAESGRFSVSRSGSTSTLTISNVTP 60

                           90       100
                   ....*....|....*....|
gi 56972362    112 KNQGYYFCSITSNSVMYFSP 131
Cdd:smart00410  61 EDSGTYTCAATNSSGSASSG 80
IGv smart00406
Immunoglobulin V-Type;
43-121 3.63e-03

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 35.44  E-value: 3.63e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56972362     43 VKLTCEVLRDT--SQGCSWLFRNSSSellQPTFIIYVSSSRSKLNDILDPNLFSARKENNKYI--LTLSKFSTKNQGYYF 118
Cdd:smart00406   2 VTLSCKFSGSTfsSYYVSWVRQPPGK---GLEWLGYIGSNGSSYYQESYKGRFTISKDTSKNDvsLTISNLRVEDTGTYY 78


                   ...
gi 56972362    119 CSI 121
Cdd:smart00406  79 CAV 81
 
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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