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Conserved domains on  [gi|30179911|ref|NP_839956|]
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paired immunoglobulin-like type 2 receptor beta isoform 2 precursor [Homo sapiens]

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 ...
 33-129 1.77e-07

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 cd05712:

Pssm-ID: 472250  Cd Length: 119  Bit Score: 48.15  E-value: 1.77e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30179911  33 YGVTQPKHLSASMGGSVEIPFSFYYPWELAIVPNVRISWRRGHFHGQSF----YSTRPPSIHKDYVNRLFLNWTEGQESG 108
Cdd:cd05712   1 WGLQMPKSVTVQEGLCVLIPCSFSYPADYWVSNPVHGYWYRGGPYPKYRppvaTNNRTREVHESTQGRFRLLGDPGKKNC 80

                        90       100
                ....*....|....*....|.
gi 30179911 109 FLRISNLRKEDQSVYFCRVEL 129
Cdd:cd05712  81 SLSISDARPEDSGKYFFRVER 101
 
Name Accession Description Interval E-value
IgV_CD33 cd05712
Immunoglobulin Variable (IgV) domain at the N-terminus of CD33 and related Siglecs (sialic ...
 33-129 1.77e-07

Immunoglobulin Variable (IgV) domain at the N-terminus of CD33 and related Siglecs (sialic acid-binding Ig-like lectins); The members here are composed of the immunoglobulin (Ig) domain at the N-terminus of Cluster of Differentiation (CD) 33 and related Siglecs (sialic acid-binding Ig-like lectins). Siglec refers to a structurally related protein family that specifically recognizes sialic acid in oligosaccharide chains of glycoproteins and glycolipids. Siglecs are type I transmembrane proteins, organized as an extracellular module composed of Ig-like domains, an N-terminal variable set of Ig-like carbohydrate recognition domains, and 1 to 16 constant Ig-like domains, followed by transmembrane and short cytoplasmic domains. Human Siglecs are classified into two subgroups, one subgroup is comprised of sialoadhesin (Siglec-1), CD22 (Siglec-2), and MAG, the other subgroup is comprised of CD33-related Siglecs which include CD33 (Siglec-3) and human Siglecs 5-11.


Pssm-ID: 409377  Cd Length: 119  Bit Score: 48.15  E-value: 1.77e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30179911  33 YGVTQPKHLSASMGGSVEIPFSFYYPWELAIVPNVRISWRRGHFHGQSF----YSTRPPSIHKDYVNRLFLNWTEGQESG 108
Cdd:cd05712   1 WGLQMPKSVTVQEGLCVLIPCSFSYPADYWVSNPVHGYWYRGGPYPKYRppvaTNNRTREVHESTQGRFRLLGDPGKKNC 80

                        90       100
                ....*....|....*....|.
gi 30179911 109 FLRISNLRKEDQSVYFCRVEL 129
Cdd:cd05712  81 SLSISDARPEDSGKYFFRVER 101
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 38-128 6.36e-05

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: 40.57  E-value: 6.36e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30179911     38 PKHLSASMGGSVEIPFSFYYPwelaivPNVRISWRRGHFhgqsfystRPPSIHKDYvnrlflNWTEGQESGFLRISNLRK 117
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGS------PPPEVTWYKQGG--------KLLAESGRF------SVSRSGSTSTLTISNVTP 60

                           90
                   ....*....|.
gi 30179911    118 EDQSVYFCRVE 128
Cdd:smart00410  61 EDSGTYTCAAT 71
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 36-127 1.06e-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: 37.44  E-value: 1.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30179911    36 TQPKHLSASMGGSVEIPFSFyypWELAIVPNVRISWRR---GHFHGQSFY---STRPPSIHKD-YVNRLFLNWTegqeSG 108
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTY---SSSMSEASTSVYWYRqppGKGPTFLIAyysNGSEEGVKKGrFSGRGDPSNG----DG 73

                          90
                  ....*....|....*....
gi 30179911   109 FLRISNLRKEDQSVYFCRV 127
Cdd:pfam07686  74 SLTIQNLTLSDSGTYTCAV 92
 
Name Accession Description Interval E-value
IgV_CD33 cd05712
Immunoglobulin Variable (IgV) domain at the N-terminus of CD33 and related Siglecs (sialic ...
 33-129 1.77e-07

Immunoglobulin Variable (IgV) domain at the N-terminus of CD33 and related Siglecs (sialic acid-binding Ig-like lectins); The members here are composed of the immunoglobulin (Ig) domain at the N-terminus of Cluster of Differentiation (CD) 33 and related Siglecs (sialic acid-binding Ig-like lectins). Siglec refers to a structurally related protein family that specifically recognizes sialic acid in oligosaccharide chains of glycoproteins and glycolipids. Siglecs are type I transmembrane proteins, organized as an extracellular module composed of Ig-like domains, an N-terminal variable set of Ig-like carbohydrate recognition domains, and 1 to 16 constant Ig-like domains, followed by transmembrane and short cytoplasmic domains. Human Siglecs are classified into two subgroups, one subgroup is comprised of sialoadhesin (Siglec-1), CD22 (Siglec-2), and MAG, the other subgroup is comprised of CD33-related Siglecs which include CD33 (Siglec-3) and human Siglecs 5-11.


Pssm-ID: 409377  Cd Length: 119  Bit Score: 48.15  E-value: 1.77e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30179911  33 YGVTQPKHLSASMGGSVEIPFSFYYPWELAIVPNVRISWRRGHFHGQSF----YSTRPPSIHKDYVNRLFLNWTEGQESG 108
Cdd:cd05712   1 WGLQMPKSVTVQEGLCVLIPCSFSYPADYWVSNPVHGYWYRGGPYPKYRppvaTNNRTREVHESTQGRFRLLGDPGKKNC 80

                        90       100
                ....*....|....*....|.
gi 30179911 109 FLRISNLRKEDQSVYFCRVEL 129
Cdd:cd05712  81 SLSISDARPEDSGKYFFRVER 101
IgV_1_PVR_like cd05718
First immunoglobulin variable (IgV) domain of poliovirus receptor (PVR, also known as CD155 ...
 35-127 9.02e-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: 46.29  E-value: 9.02e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30179911  35 VTQPKHLSASMGGSVEIPFSFYYPWELAIVpnvRISWRRGHFHGQS----FYSTRPPSIHKDYVNRL-FLNWTEGQESGF 109
Cdd:cd05718   3 VQVPTEVTGFLGGSVTLPCSLTSPGTTKIT---QVTWMKIGAGSSQnvavFHPQYGPSVPNPYAERVeFLAARLGLRNAT 79

                        90
                ....*....|....*...
gi 30179911 110 LRISNLRKEDQSVYFCRV 127
Cdd:cd05718  80 LRIRNLRVEDEGNYICEF 97
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 38-128 6.36e-05

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: 40.57  E-value: 6.36e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30179911     38 PKHLSASMGGSVEIPFSFYYPwelaivPNVRISWRRGHFhgqsfystRPPSIHKDYvnrlflNWTEGQESGFLRISNLRK 117
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGS------PPPEVTWYKQGG--------KLLAESGRF------SVSRSGSTSTLTISNVTP 60

                           90
                   ....*....|.
gi 30179911    118 EDQSVYFCRVE 128
Cdd:smart00410  61 EDSGTYTCAAT 71
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 35-147 2.95e-04

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: 39.24  E-value: 2.95e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30179911  35 VTQ-PKHLSASMGGSVEI------PFSFYYpwelaivpnvrISW---RRGH-----FHGQSFYSTRPPSIHKDYVNRLfl 99
Cdd:cd00099   1 VTQsPRSLSVQEGESVTLscevssSFSSTY-----------IYWyrqKPGQgpeflIYLSSSKGKTKGGVPGRFSGSR-- 67

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 30179911 100 nwtEGQESGFLRISNLRKEDQSVYFCRVeldTRRSGRQQLQSIKGTKL 147
Cdd:cd00099  68 ---DGTSSFSLTISNLQPEDSGTYYCAV---SESGGTDKLTFGSGTRL 109
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 36-127 1.06e-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: 37.44  E-value: 1.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30179911    36 TQPKHLSASMGGSVEIPFSFyypWELAIVPNVRISWRR---GHFHGQSFY---STRPPSIHKD-YVNRLFLNWTegqeSG 108
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTY---SSSMSEASTSVYWYRqppGKGPTFLIAyysNGSEEGVKKGrFSGRGDPSNG----DG 73

                          90
                  ....*....|....*....
gi 30179911   109 FLRISNLRKEDQSVYFCRV 127
Cdd:pfam07686  74 SLTIQNLTLSDSGTYTCAV 92
IgV_CD2_like_N cd05775
N-terminal immunoglobulin (Ig)-like domain of T-cell surface antigen CD2, and similar domains; ...
 43-127 1.26e-03

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: 36.94  E-value: 1.26e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30179911  43 ASMGGSVeipfsFYYPWELAiVPNVRISWRRGHFHGQSFYSTRPPSIHKDYVNRLFLNwtegQESGFLRISNLRKEDQSV 122
Cdd:cd05775   7 GALGGNV-----TLTISSLQ-DDIDEIKWKKTKDKIVEWENNIGPTYFGSFKDRVLLD----KESGSLTIKNLTKEDSGT 76


                ....*
gi 30179911 123 YFCRV 127
Cdd:cd05775  77 YELEI 81
IgV_1_Nectin-2_NecL-5_like_CD112_CD155 cd20989
First immunoglobulin variable (IgV) domain of nectin-2, nectin-like protein 5, and similar ...
 35-125 2.57e-03

First immunoglobulin variable (IgV) domain of nectin-2, nectin-like protein 5, and similar domains; The members here are composed of the second immunoglobulin (Ig) domain of nectin-2 (also known as poliovirus receptor related protein 2 or Cluster of Differentiation 112 (CD112)), nectin-like protein 5 (CD155), and similar proteins. Nectins and Nectin-like molecules are a family of Ca(2+)-independent immunoglobulin-like transmembrane glycoproteins belonging to the class of adhesion receptors, consisting of nine members (nectins 1 through 4 and nectin-like proteins 1 through 5). Nectins are synaptic cell adhesion molecules (CAMs) which facilitate adhesion and signaling at various intracellular junctions. Nectins form homophilic cis-dimers, followed by homophilic and heterophilic trans-dimers involved in cell-cell adhesion. Nectin-2 and nectin-3 localize at Sertoli-spermatid junctions where they form heterophilic trans-interactions between the cells that are essential for the formation and maintenance of the junctions and for spermatid development. CD155 is the fifth member in the nectin-like molecule family, and functions as the receptor of poliovirus; therefore, CD155 is also referred to as Necl-5, or PVR. In contrast to all other family members, CD155 lacks self-adhesion capacity, yet it shares with nectins the feature to interact with other nectins. For instance, CD155 heterophilically trans-interacts with nectin-3, thereby contributing significantly to the establishment of adherens junctions between epithelial cells. This group belongs to the Constant 1 (C1)-set of IgSF domains, which has one beta-sheet that is formed by strands A-B-E-D and the other strands by G-F-C-C'.


Pssm-ID: 409581  Cd Length: 112  Bit Score: 36.40  E-value: 2.57e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30179911  35 VTQPKHLSASMGGSVEIPFSFYYPwelaiVPNVRIS---WRRGHFHG--QSFYSTRPPSIHKDyvNRL-FLNWTEGQE-- 106
Cdd:cd20989   3 VQVPPEVRGFLGGSVTLPCHLLPP-----NMVTHVSqvtWQRHDEHGsvAVFHPKQGPSFPES--ERLsFVAARLGAElr 75

                        90
                ....*....|....*....
gi 30179911 107 SGFLRISNLRKEDQSVYFC 125
Cdd:cd20989  76 NASLAMFGLRVEDEGNYTC 94
IGv smart00406
Immunoglobulin V-Type;
65-125 6.30e-03

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 34.67  E-value: 6.30e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 30179911     65 PNVRISWRRgHFHGQ------SFYSTRPPSIHKDYVNRLFLNWTEGQESGFLRISNLRKEDQSVYFC 125
Cdd:smart00406  14 SSYYVSWVR-QPPGKglewlgYIGSNGSSYYQESYKGRFTISKDTSKNDVSLTISNLRVEDTGTYYC 79
 
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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