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Conserved domains on  [gi|1937369399|ref|NP_037253|]
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T-cell-specific surface glycoprotein CD28 precursor [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 ...
 22-138 4.25e-65

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 cd20925:

Pssm-ID: 472250  Cd Length: 117  Bit Score: 197.09  E-value: 4.25e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369399  22 ILVKQSPLLVVDNNEVSLSCRYSYNLLAKEFRASLYKGVNSDVEVCVGNGNFTYQPQFRPNVGFNCDGNFDNETVTFRLW 101
Cdd:cd20925     1 ILVKQSPMLVVYNNAVNLSCKYTYNLFSKEFRASLHKGLDSAVEVCVVYGNYSQQLQVYSNTGFNCDGKLGNESVTFYLW 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1937369399 102 NLHVNHTDIYFCKIEVMYPPPYLDNEKSNGTIIHIKE 138
Cdd:cd20925    81 NLYVNQTDIYFCKIEVMYPPPYLDNEKSNGTIIHVKE 117
 
Name Accession Description Interval E-value
IgV_CD28 cd20925
Immunoglobulin Variable (IgV) domain Cluster of Differentiation (CD) 28; The members here are ...
 22-138 4.25e-65

Immunoglobulin Variable (IgV) domain Cluster of Differentiation (CD) 28; The members here are composed of the immunoglobulin variable region (IgV) of Cluster of Differentiation (CD) 28). CD28 is one of the proteins expressed on T cells that provide co-stimulatory signals required for T cell activation and survival. CD28 is the receptor for CD80 (B7.1) and CD86 (B7.2) proteins. CD28 consists of a paired V-set of immunoglobulin (Ig) superfamily domains attached to single-transmembrane domains and cytoplasmic domains that contain the MYPPY motif, which is involved in binding B7.1 or B7.2. CD28 is very similar to CTLA-4 (cytotoxic T-lymphocyte-associated protein 4, also known as CD152 (cluster of differentiation 152)), which is involved in the regulation of T cell response, acting as an inhibitor of intracellular signaling. CTLA-4 also binds the B7 molecules (B7.1 and B7.2) with a higher affinity than does CD28. The B7/CTLA-4 interaction generates inhibitory signals down-regulating the response, and may prevent T cell activation by weak TCR signals. CD28 and CTLA-4 then elicit opposing signals in the regulation of T cell responsiveness and homeostasis. The IgSF is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. The two sheets are linked together by a conserved disulfide bond between B strand and F strand. 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. The N-terminal Ig-like domain of CD28 is a member of the V-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C'-C" in the other. However, each CD28-B7 family member is slightly different, some have an IgV domain which lacks an A' or C" strand.


Pssm-ID: 409519  Cd Length: 117  Bit Score: 197.09  E-value: 4.25e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369399  22 ILVKQSPLLVVDNNEVSLSCRYSYNLLAKEFRASLYKGVNSDVEVCVGNGNFTYQPQFRPNVGFNCDGNFDNETVTFRLW 101
Cdd:cd20925     1 ILVKQSPMLVVYNNAVNLSCKYTYNLFSKEFRASLHKGLDSAVEVCVVYGNYSQQLQVYSNTGFNCDGKLGNESVTFYLW 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1937369399 102 NLHVNHTDIYFCKIEVMYPPPYLDNEKSNGTIIHIKE 138
Cdd:cd20925    81 NLYVNQTDIYFCKIEVMYPPPYLDNEKSNGTIIHVKE 117
IGv smart00406
Immunoglobulin V-Type;
37-115 5.55e-09

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 51.23  E-value: 5.55e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369399   37 VSLSCRYSYNLLAKEFRASLYKGVNSDVEVCVGNGNFT---YQPQFRPnvGFNCDGNFDNETVTFRLWNLHVNHTDIYFC 113
Cdd:smart00406   2 VTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIGSNGssyYQESYKG--RFTISKDTSKNDVSLTISNLRVEDTGTYYC 79


                   ..
gi 1937369399  114 KI 115
Cdd:smart00406  80 AV 81
V-set_2 pfam15910
ICOS V-set domain; This family contains divergent V-set ig domains found in the ICOS protein.
 34-139 7.50e-09

ICOS V-set domain; This family contains divergent V-set ig domains found in the ICOS protein.


Pssm-ID: 464936  Cd Length: 112  Bit Score: 51.72  E-value: 7.50e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369399  34 NNEVSLSCRYSYNLlaKEFRASLYKGVNS--DVEVCVGNGNftyqPQFRPNVGFnCDGNFDNETVTFRLWNLHVNHTDIY 111
Cdd:pfam15910  12 NGGVQILCKYPETV--QQFKMQLLKGREIlcDLTKTKGSGN----TVSIKNVTL-CQSQLSNNSVSFFLYNLDSSHASYY 84

                          90       100
                  ....*....|....*....|....*...
gi 1937369399 112 FCKIEVMYPPPYLDNEKSnGTIIHIKEK 139
Cdd:pfam15910  85 FCCLSIFDPPPFIHCILS-GEYLYIYES 111
 
Name Accession Description Interval E-value
IgV_CD28 cd20925
Immunoglobulin Variable (IgV) domain Cluster of Differentiation (CD) 28; The members here are ...
 22-138 4.25e-65

Immunoglobulin Variable (IgV) domain Cluster of Differentiation (CD) 28; The members here are composed of the immunoglobulin variable region (IgV) of Cluster of Differentiation (CD) 28). CD28 is one of the proteins expressed on T cells that provide co-stimulatory signals required for T cell activation and survival. CD28 is the receptor for CD80 (B7.1) and CD86 (B7.2) proteins. CD28 consists of a paired V-set of immunoglobulin (Ig) superfamily domains attached to single-transmembrane domains and cytoplasmic domains that contain the MYPPY motif, which is involved in binding B7.1 or B7.2. CD28 is very similar to CTLA-4 (cytotoxic T-lymphocyte-associated protein 4, also known as CD152 (cluster of differentiation 152)), which is involved in the regulation of T cell response, acting as an inhibitor of intracellular signaling. CTLA-4 also binds the B7 molecules (B7.1 and B7.2) with a higher affinity than does CD28. The B7/CTLA-4 interaction generates inhibitory signals down-regulating the response, and may prevent T cell activation by weak TCR signals. CD28 and CTLA-4 then elicit opposing signals in the regulation of T cell responsiveness and homeostasis. The IgSF is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. The two sheets are linked together by a conserved disulfide bond between B strand and F strand. 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. The N-terminal Ig-like domain of CD28 is a member of the V-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C'-C" in the other. However, each CD28-B7 family member is slightly different, some have an IgV domain which lacks an A' or C" strand.


Pssm-ID: 409519  Cd Length: 117  Bit Score: 197.09  E-value: 4.25e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369399  22 ILVKQSPLLVVDNNEVSLSCRYSYNLLAKEFRASLYKGVNSDVEVCVGNGNFTYQPQFRPNVGFNCDGNFDNETVTFRLW 101
Cdd:cd20925     1 ILVKQSPMLVVYNNAVNLSCKYTYNLFSKEFRASLHKGLDSAVEVCVVYGNYSQQLQVYSNTGFNCDGKLGNESVTFYLW 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1937369399 102 NLHVNHTDIYFCKIEVMYPPPYLDNEKSNGTIIHIKE 138
Cdd:cd20925    81 NLYVNQTDIYFCKIEVMYPPPYLDNEKSNGTIIHVKE 117
IgV_CTLA-4 cd05721
Immunoglobulin Variable (IgV) domain of cytotoxic T lymphocyte-associated antigen 4 (CTLA-4); ...
 38-136 8.11e-10

Immunoglobulin Variable (IgV) domain of cytotoxic T lymphocyte-associated antigen 4 (CTLA-4); The members here are composed of the variable(v)-type immunoglobulin (Ig) domain found in cytotoxic T lymphocyte-associated antigen 4 (CTLA-4). CTLA-4 is involved in the regulation of T cell response, acting as an inhibitor of intracellular signaling. CTLA-4 is similar to CD28, a T cell co-receptor protein that recognizes the B7 proteins (CD80 and CD86). CD28 binding of the B7 proteins occurs after the presentation of antigen to the T cell receptor (TCR) via the peptide-MHC complex on the surface of an antigen presenting cell (APC). CTLA-4 also binds the B7 molecules with a higher affinity than does CD28. The B7/CTLA-4 interaction generates inhibitory signals down-regulating the response, and may prevent T cell activation by weak TCR signals. CD28 and CTLA-4 then elicit opposing signals in the regulation of T cell responsiveness and homeostasis. T cell activation leads to increased CTLA-4 gene expression and trafficking of CTLA-4 protein to the cell surface. CTLA-4 is not detected on the T-cell surface until 24 hours after activation. Covalent dimerization of CTLA-4 has been shown to be required for its high binding avidity, although each CTLA-4 monomer contains a binding site for CD80 and CD86.


Pssm-ID: 409386  Cd Length: 115  Bit Score: 54.62  E-value: 8.11e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369399  38 SLSCRYSYNLLAKEFRASLYKGVNSDV-EVCVGngnfTYQpqFRPNVGF----NCDGNFDNETVTFRLWNLHVNHTDIYF 112
Cdd:cd05721    17 SFVCEYASSGNATEVRVTVLRQADSQMtEVCAA----TYT--MGNELTFlddsICTGTSSGNQVNLTIQGLRAMDTGLYI 90

                          90       100
                  ....*....|....*....|....
gi 1937369399 113 CKIEVMYPPPYLDNeKSNGTIIHI 136
Cdd:cd05721    91 CKVELMYPPPYYVG-MGNGTQIYV 113
IGv smart00406
Immunoglobulin V-Type;
37-115 5.55e-09

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 51.23  E-value: 5.55e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369399   37 VSLSCRYSYNLLAKEFRASLYKGVNSDVEVCVGNGNFT---YQPQFRPnvGFNCDGNFDNETVTFRLWNLHVNHTDIYFC 113
Cdd:smart00406   2 VTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIGSNGssyYQESYKG--RFTISKDTSKNDVSLTISNLRVEDTGTYYC 79


                   ..
gi 1937369399  114 KI 115
Cdd:smart00406  80 AV 81
V-set_2 pfam15910
ICOS V-set domain; This family contains divergent V-set ig domains found in the ICOS protein.
 34-139 7.50e-09

ICOS V-set domain; This family contains divergent V-set ig domains found in the ICOS protein.


Pssm-ID: 464936  Cd Length: 112  Bit Score: 51.72  E-value: 7.50e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369399  34 NNEVSLSCRYSYNLlaKEFRASLYKGVNS--DVEVCVGNGNftyqPQFRPNVGFnCDGNFDNETVTFRLWNLHVNHTDIY 111
Cdd:pfam15910  12 NGGVQILCKYPETV--QQFKMQLLKGREIlcDLTKTKGSGN----TVSIKNVTL-CQSQLSNNSVSFFLYNLDSSHASYY 84

                          90       100
                  ....*....|....*....|....*...
gi 1937369399 112 FCKIEVMYPPPYLDNEKSnGTIIHIKEK 139
Cdd:pfam15910  85 FCCLSIFDPPPFIHCILS-GEYLYIYES 111
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 27-115 6.11e-04

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: 38.21  E-value: 6.11e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369399  27 SPLLVVDNNEVSLSCRYSYNLLAKEFRASLYKGVNSDVEVCVGNGNFTYQPQFRPNVGFNCDGNFDNETVTFRLWNLHVN 106
Cdd:pfam07686   4 REVTVALGGSVTLPCTYSSSMSEASTSVYWYRQPPGKGPTFLIAYYSNGSEEGVKKGRFSGRGDPSNGDGSLTIQNLTLS 83


                  ....*....
gi 1937369399 107 HTDIYFCKI 115
Cdd:pfam07686  84 DSGTYTCAV 92
 
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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