NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|56789732|gb|AAH88439|]
View 

LOC500947 protein, partial [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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 67-142 2.52e-06

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 cd05775:

Pssm-ID: 472250  Cd Length: 98  Bit Score: 44.26  E-value: 2.52e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56789732  67 PTIEWEYTPnwgvQKIVEWKPGTPANVSQSHRDRVcTFD--NGSIQLFSVGVRDSGYYVITVTEHPGSSQSGTILLHV 142
Cdd:cd05775  25 DEIKWKKTK----DKIVEWENNIGPTYFGSFKDRV-LLDkeSGSLTIKNLTKEDSGTYELEITSTNGKVLSSKFTLEV 97
 
Name Accession Description Interval E-value
IgV_CD2_like_N cd05775
N-terminal immunoglobulin (Ig)-like domain of T-cell surface antigen CD2, and similar domains; ...
 67-142 2.52e-06

N-terminal immunoglobulin (Ig)-like domain of T-cell surface antigen CD2, and similar domains; The members here are composed of the N-terminal immunoglobulin (Ig)-like domain (or domain 1) of T-cell surface antigen Clusters of Differentiation (CD) 2 and similar proteins. CD2 is a T-cell specific surface glycoprotein and is critically important for mediating adhesion between T cells and antigen-presenting cells or between cytolytic T cells and target cells. CD2 is located on chromosome 1 at 1p13 in humans and on chromosome 3 in mice. CD2 contains an extracellular domain with two or Ig-like domains, a single transmembrane segment, and a cytoplasmic region rich in proline and basic residues.


Pssm-ID: 409431  Cd Length: 98  Bit Score: 44.26  E-value: 2.52e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56789732  67 PTIEWEYTPnwgvQKIVEWKPGTPANVSQSHRDRVcTFD--NGSIQLFSVGVRDSGYYVITVTEHPGSSQSGTILLHV 142
Cdd:cd05775  25 DEIKWKKTK----DKIVEWENNIGPTYFGSFKDRV-LLDkeSGSLTIKNLTKEDSGTYELEITSTNGKVLSSKFTLEV 97
 
Name Accession Description Interval E-value
IgV_CD2_like_N cd05775
N-terminal immunoglobulin (Ig)-like domain of T-cell surface antigen CD2, and similar domains; ...
 67-142 2.52e-06

N-terminal immunoglobulin (Ig)-like domain of T-cell surface antigen CD2, and similar domains; The members here are composed of the N-terminal immunoglobulin (Ig)-like domain (or domain 1) of T-cell surface antigen Clusters of Differentiation (CD) 2 and similar proteins. CD2 is a T-cell specific surface glycoprotein and is critically important for mediating adhesion between T cells and antigen-presenting cells or between cytolytic T cells and target cells. CD2 is located on chromosome 1 at 1p13 in humans and on chromosome 3 in mice. CD2 contains an extracellular domain with two or Ig-like domains, a single transmembrane segment, and a cytoplasmic region rich in proline and basic residues.


Pssm-ID: 409431  Cd Length: 98  Bit Score: 44.26  E-value: 2.52e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56789732  67 PTIEWEYTPnwgvQKIVEWKPGTPANVSQSHRDRVcTFD--NGSIQLFSVGVRDSGYYVITVTEHPGSSQSGTILLHV 142
Cdd:cd05775  25 DEIKWKKTK----DKIVEWENNIGPTYFGSFKDRV-LLDkeSGSLTIKNLTKEDSGTYELEITSTNGKVLSSKFTLEV 97
IgV_CEACAM_like cd05741
Immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion ...
 81-142 6.63e-04

Immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and similar proteins; The members here are composed of the immunoglobulin (Ig)-like domain in carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and related domains. The CEA family is a group of anchored or secreted glycoproteins, expressed by epithelial cells, leukocytes, endothelial cells and placenta. The CEA family is divided into the CEACAM and pregnancy-specific glycoprotein (PSG) subfamilies. This group represents the CEACAM subfamily. CEACAM1 has many important cellular functions: it is a cell adhesion molecule and a signaling molecule that regulates the growth of tumor cells, an angiogenic factor, and a receptor for bacterial and viral pathogens, including mouse hepatitis virus (MHV). In mice, four isoforms of CEACAM1 generated by alternative splicing have either two (D1, D4) or four (D1-D4) Ig-like domains on the cell surface. This family corresponds to the D1 Ig-like domain. Also belonging to this group is the N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84-like family. The SLAM family is a group of immune-cell specific receptors that can regulate both adaptive and innate immune responses. SLAM family proteins are organized as an extracellular domain with having two or four Ig-like domains, a single transmembrane segment, and a cytoplasmic region having Tyr-based motifs. The extracellular domain is organized as a membrane-distal Ig variable (IgV) domain that is responsible for ligand recognition and a membrane-proximal truncated Ig constant-2 (IgC2) domain.


Pssm-ID: 409403  Cd Length: 102  Bit Score: 37.88  E-value: 6.63e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56789732  81 KIVEWKPGTPAN-VSQSHRDRVCTFDNGSIQLFSVGVRDSGYYVITVTEHPGSSQSGTILLHV 142
Cdd:cd05741  40 EIAEYENSSDEFrAGSAFSGREYIYTNGSLLIQNITLSDTGFYTLESTNIGGKTESATFQLHV 102
IgV_CEACAM_D1 cd05774
First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion ...
 48-142 8.81e-04

First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM); The members here are composed of the immunoglobulin (Ig)-like domain 1 in carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) proteins. The CEA family is a group of anchored or secreted glycoproteins, expressed by epithelial cells, leukocytes, endothelial cells, and placenta. The CEA family is divided into the CEACAM and pregnancy-specific glycoprotein (PSG) subfamilies. This group represents the CEACAM subfamily. CEACAM1 has many important cellular functions: it is a cell adhesion molecule and a signaling molecule that regulates the growth of tumor cells, an angiogenic factor, and a receptor for bacterial and viral pathogens, including mouse hepatitis virus (MHV). In mice, four isoforms of CEACAM1 generated by alternative splicing have either two (D1, D4) or four (D1-D4) Ig-like domains on the cell surface.


Pssm-ID: 409430  Cd Length: 105  Bit Score: 37.25  E-value: 8.81e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56789732  48 NATVQEDILLSVdyicHGVPTIEWEYTpnW--GV-----QKIVEWKPGTpaNVSQ---SHRDRVCTFDNGSIQLFSVGVR 117
Cdd:cd05774   9 QVAEGENVLLLV----HNLPENLLAYA--WykGKtvspnFLIASYIIST--NSSTpgpAYSGRETIYPNGSLLIQNVTQK 80

                        90       100
                ....*....|....*....|....*
gi 56789732 118 DSGYYVITVTEHPGSSQSGTILLHV 142
Cdd:cd05774  81 DTGFYTLQTITADLQTEQASVHLQV 105
IgV_1_PVR_like cd05718
First immunoglobulin variable (IgV) domain of poliovirus receptor (PVR, also known as CD155 ...
 69-142 5.98e-03

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: 35.12  E-value: 5.98e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56789732  69 IEWEYTPNWGVQKIVEWKPGTPANVSQSHRDRV------CTFDNGSIQLFSVGVRDSGYYVITVTEHPGSSQSGTILLHV 142
Cdd:cd05718  34 VTWMKIGAGSSQNVAVFHPQYGPSVPNPYAERVeflaarLGLRNATLRIRNLRVEDEGNYICEFATFPQGNRQGTTWLRV 113
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH