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Conserved domains on  [gi|29244314|ref|NP_808457|]
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V-set and immunoglobulin domain-containing protein 4 precursor [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 ...
 21-137 1.58e-68

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 cd16089:

Pssm-ID: 472250  Cd Length: 117  Bit Score: 208.15  E-value: 1.58e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29244314  21 PTLKTPESVTGTWKGDVKIQCIYDPLRGYRQVLVKWLVRHGSDSVTIFLRDSTGDHIQQAKYRGRLKVSHKVPGDVSLQI 100
Cdd:cd16089   1 PILEGPESITGPWKGSVNLPCTYVPEEGYTQVLVKWLVQRDSDPVTIFLRDSSGDHIQQAKYRGRLEVSKDTPGDVSLQL 80

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 29244314 101 NTLQMDDRNHYTCEVTWQTPDGNQVIRDKIIELRVRK 137
Cdd:cd16089  81 DTLEMDDRGHYTCQVTWQTPDGNLIVREKTTELRVQK 117
 
Name Accession Description Interval E-value
IgV_CRIg cd16089
Immunoglobulin variable (IgV)-like domain in complement receptor of the immunoglobulin ...
 21-137 1.58e-68

Immunoglobulin variable (IgV)-like domain in complement receptor of the immunoglobulin superfamily (CRIg); The members here are composed of the immunoglobulin variable (IgV) region of the complement receptor of the immunoglobulin superfamily (CRIg). The N-terminal domain of CRIg (also known as Z39Ig and V-set and Ig domain-containing 4 (VSIG4) belongs to the IgV family of immunoglobulin-like domains while the C-terminal domain of CRIg belongs to the IgC family of immunoglobulin-like domains. Like all members of this family, the CRIg domain contains two beta-sheets: one composed of strands A', G, F, C, C' and C", and the other of strands B, E and D. The complement system is an important part of the innate immune system and is required for removal of pathogens from the bloodstream. After exposure to pathogens, the third component of the complement system, C3, is cleaved to C3b which, after recruitment of factor B, initiates formation of the alternative pathway convertases. CRIg, a complement receptor expressed on macrophages, binds to C3b and iC3b mediating phagocytosis of the particles. It is also a potent inhibitor of the alternative pathway convertases and a negative regulator of T cell activation. 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, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, 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.


Pssm-ID: 409510  Cd Length: 117  Bit Score: 208.15  E-value: 1.58e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29244314  21 PTLKTPESVTGTWKGDVKIQCIYDPLRGYRQVLVKWLVRHGSDSVTIFLRDSTGDHIQQAKYRGRLKVSHKVPGDVSLQI 100
Cdd:cd16089   1 PILEGPESITGPWKGSVNLPCTYVPEEGYTQVLVKWLVQRDSDPVTIFLRDSSGDHIQQAKYRGRLEVSKDTPGDVSLQL 80

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 29244314 101 NTLQMDDRNHYTCEVTWQTPDGNQVIRDKIIELRVRK 137
Cdd:cd16089  81 DTLEMDDRGHYTCQVTWQTPDGNLIVREKTTELRVQK 117
IGv smart00406
Immunoglobulin V-Type;
49-115 6.29e-04

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 37.75  E-value: 6.29e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 29244314     49 YRQ---VLVKWLVRHGSDSVTIflrdstgdhiQQAKYRGRLKVSHKV-PGDVSLQINTLQMDDRNHYTCEV 115
Cdd:smart00406  21 VRQppgKGLEWLGYIGSNGSSY----------YQESYKGRFTISKDTsKNDVSLTISNLRVEDTGTYYCAV 81
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 25-115 1.16e-03

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: 37.82  E-value: 1.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29244314    25 TPESVTGTWKGDVKIQCIYDPLRGYRQVLVKWLVR---HGSDSVTIFLRDSTGDHIQQAKYRGRlkvSHKVPGDVSLQIN 101
Cdd:pfam07686   2 TPREVTVALGGSVTLPCTYSSSMSEASTSVYWYRQppgKGPTFLIAYYSNGSEEGVKKGRFSGR---GDPSNGDGSLTIQ 78

                          90
                  ....*....|....
gi 29244314   102 TLQMDDRNHYTCEV 115
Cdd:pfam07686  79 NLTLSDSGTYTCAV 92
 
Name Accession Description Interval E-value
IgV_CRIg cd16089
Immunoglobulin variable (IgV)-like domain in complement receptor of the immunoglobulin ...
 21-137 1.58e-68

Immunoglobulin variable (IgV)-like domain in complement receptor of the immunoglobulin superfamily (CRIg); The members here are composed of the immunoglobulin variable (IgV) region of the complement receptor of the immunoglobulin superfamily (CRIg). The N-terminal domain of CRIg (also known as Z39Ig and V-set and Ig domain-containing 4 (VSIG4) belongs to the IgV family of immunoglobulin-like domains while the C-terminal domain of CRIg belongs to the IgC family of immunoglobulin-like domains. Like all members of this family, the CRIg domain contains two beta-sheets: one composed of strands A', G, F, C, C' and C", and the other of strands B, E and D. The complement system is an important part of the innate immune system and is required for removal of pathogens from the bloodstream. After exposure to pathogens, the third component of the complement system, C3, is cleaved to C3b which, after recruitment of factor B, initiates formation of the alternative pathway convertases. CRIg, a complement receptor expressed on macrophages, binds to C3b and iC3b mediating phagocytosis of the particles. It is also a potent inhibitor of the alternative pathway convertases and a negative regulator of T cell activation. 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, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, 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.


Pssm-ID: 409510  Cd Length: 117  Bit Score: 208.15  E-value: 1.58e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29244314  21 PTLKTPESVTGTWKGDVKIQCIYDPLRGYRQVLVKWLVRHGSDSVTIFLRDSTGDHIQQAKYRGRLKVSHKVPGDVSLQI 100
Cdd:cd16089   1 PILEGPESITGPWKGSVNLPCTYVPEEGYTQVLVKWLVQRDSDPVTIFLRDSSGDHIQQAKYRGRLEVSKDTPGDVSLQL 80

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 29244314 101 NTLQMDDRNHYTCEVTWQTPDGNQVIRDKIIELRVRK 137
Cdd:cd16089  81 DTLEMDDRGHYTCQVTWQTPDGNLIVREKTTELRVQK 117
IgV_1_PVR_like cd05718
First immunoglobulin variable (IgV) domain of poliovirus receptor (PVR, also known as CD155 ...
 26-135 2.30e-07

First immunoglobulin variable (IgV) domain of poliovirus receptor (PVR, also known as CD155 and necl-5), and similar domains; The members here are composed of the first immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155 and nectin-like protein 5 (necl-5)). Poliovirus (PV) binds to its cellular receptor (PVR/CD155) to initiate infection. CD155 is a membrane-anchored, single-span glycoprotein; its extracellular region has three Ig-like domains. There are four different isotypes of CD155 (referred to as alpha, beta, gamma, and delta), that result from alternate splicing of the CD155 mRNA, and have identical extracellular domains. CD155-beta and CD155-gamma are secreted; CD155-alpha and CD155-delta are membrane-bound and function as PV receptors. The virus recognition site is contained in the amino-terminal domain, D1. Having the virus attachment site on the receptor distal from the plasma membrane may be important for successful initiation of infection of cells by the virus. CD155 binds in the poliovirus "canyon" with a footprint similar to that of the intercellular adhesion molecule-1 receptor on human rhinoviruses. This group also includes the first Ig-like domain of nectin-1 (also known as poliovirus receptor related protein(PVRL)1; CD111), nectin-3 (also known as PVRL 3), nectin-4 (also known as PVRL4; LNIR receptor)and DNAX accessory molecule 1 (DNAM-1; CD226).


Pssm-ID: 409383  Cd Length: 113  Bit Score: 48.21  E-value: 2.30e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29244314  26 PESVTGTWKGDVKIQCIYDPLRGYRQVLVKWLVRHG--SDSVTIFlRDSTGDHIqQAKYRGRLKVSHKVPG--DVSLQIN 101
Cdd:cd05718   6 PTEVTGFLGGSVTLPCSLTSPGTTKITQVTWMKIGAgsSQNVAVF-HPQYGPSV-PNPYAERVEFLAARLGlrNATLRIR 83

                        90       100       110
                ....*....|....*....|....*....|....
gi 29244314 102 TLQMDDRNHYTCEVTwQTPDGNqviRDKIIELRV 135
Cdd:cd05718  84 NLRVEDEGNYICEFA-TFPQGN---RQGTTWLRV 113
Ig_LP_like cd05877
Immunoglobulin (Ig)-like domain of human cartilage link protein (LP), and similar domains; The ...
 35-136 4.05e-05

Immunoglobulin (Ig)-like domain of human cartilage link protein (LP), and similar domains; The members here are composed of the immunoglobulin (Ig)-like domain similar to that found in human cartilage link protein (LP; also called hyaluronan and proteoglycan link protein). In cartilage, chondroitin-keratan sulfate proteoglycan (CSPG), aggrecan, forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


Pssm-ID: 409461  Cd Length: 117  Bit Score: 41.93  E-value: 4.05e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29244314  35 GDVKIQCIYD---PLRGYRQVLVKW--LVRHGSDSVTIFLrdSTGDHIQQ-AKYRGRLKVSHKVPGDVSLQINTLQMDDR 108
Cdd:cd05877  13 GNVTLPCRYHyepELSAPRKIRVKWtkLEVDYAKEEDVLV--AIGTRHKSyGSYQGRVFLRRADDLDASLVITDLRLEDY 90

                        90       100       110
                ....*....|....*....|....*....|
gi 29244314 109 NHYTCEVTwqtpDGnqvIRDK--IIELRVR 136
Cdd:cd05877  91 GRYRCEVI----DG---LEDEsvVVALRLR 113
IGv smart00406
Immunoglobulin V-Type;
49-115 6.29e-04

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 37.75  E-value: 6.29e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 29244314     49 YRQ---VLVKWLVRHGSDSVTIflrdstgdhiQQAKYRGRLKVSHKV-PGDVSLQINTLQMDDRNHYTCEV 115
Cdd:smart00406  21 VRQppgKGLEWLGYIGSNGSSY----------YQESYKGRFTISKDTsKNDVSLTISNLRVEDTGTYYCAV 81
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 25-115 1.16e-03

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: 37.82  E-value: 1.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29244314    25 TPESVTGTWKGDVKIQCIYDPLRGYRQVLVKWLVR---HGSDSVTIFLRDSTGDHIQQAKYRGRlkvSHKVPGDVSLQIN 101
Cdd:pfam07686   2 TPREVTVALGGSVTLPCTYSSSMSEASTSVYWYRQppgKGPTFLIAYYSNGSEEGVKKGRFSGR---GDPSNGDGSLTIQ 78

                          90
                  ....*....|....
gi 29244314   102 TLQMDDRNHYTCEV 115
Cdd:pfam07686  79 NLTLSDSGTYTCAV 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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