Summary: Immunoglobulin V-set domain
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Immunoglobulin V-set domain Edit Wikipedia article
|Immunoglobulin V-set domain|
Structure of phosphocholine binding immunoglobulin Fab McPC603.
V-set domains are Ig-like domains resembling the antibody variable domain. V-set domains are found in diverse protein families, including immunoglobulin light and heavy chains; in several T-cell receptors such as CD2 (Cluster of Differentiation 2), CD4, CD80, and CD86; in myelin membrane adhesion molecules; in junction adhesion molecules (JAM); in tyrosine-protein kinase receptors; and in the programmed cell death protein 1 (PD1).
Human proteins containing this domain
ACAM; ACAN; ADAMTSL1; AGC1; AMICA1; BCAM; BCAN; BGP; BGPc; BT3.3; BTN1A1; BTN2A1; BTN2A2; BTN2A3; BTN3A1; BTN3A2; BTN3A3; BTNL2; BTNL3; BTNL8; BTNL9; C10orf54; C1orf32; C9orf94; CADM1; CADM2; CADM3; CADM4; CD2; CD226; CD274; CD276; CD300A; CD300C; CD300D; CD300E; CD300LB; CD300LF; CD300LG; CD33; CD3G; CD7; CD79A; CD79B; CD80; CD83; CD86; CD8A; CD8B; CD8B1; CD96; CEACAM1; CEACAM16; CEACAM19; CEACAM21; CEACAM3; CEACAM4; CEACAM5; CEACAM6; CEACAM7; CEACAM8; CHL1; CREA7-4; CRTAM; CSF1R; CTLA4; CXADR; ERMAP; ESAM; F11R; FCAMR; FCRL2; FKSG87; GLUDP5; GPA33; HAPLN1; HAPLN2; HAPLN3; HAPLN4; HAVCR1; HEPACAM; HHLA2; HSPG2; ICOSLG; IGHA1; IGHA2; IGHD; IGHG1; IGHG3; IGHM; IGHV1-69; IGHV4-31; IGHV7-81; IGKC; IGKV1-5; IGKV2-24; IGL@; IGLC1; IGLV2-14; IGLV3-21; IGLV3-25; IGLV4-3; IGLV5-52; IGLV6-57; IGSF11; IGSF2; IGSF3; IGSF6; IGSF8; IGSF9; IL18R1; IREM2; IREM3; JAM2; JAM3; KDR; KIRREL; KIRREL2; KIRREL3; LAG3; LOC253012; LOC402482; MAG; MGC33530; MOG; MPZ; MPZL1; MPZL2; MXRA8; MYBPC3; NCA; NCR2; NCR3; NPHS1; OBSL1; OPCML; P0; PDCD1; PIGR; PILRA; PILRB; PRODH2; PSG1; PSG10; PSG11; PSG11s'; PSG2; PSG3; PSG4; PSG5; PSG6; PSG7; PSG8; PSG9; PTGFRN; PTPN1L; PVR; PVRL1; PVRL2; PVRL3; PVRL4; SCN2B; SCN3B; SCN4B; SEMA3D; SIGLEC1; SIGLEC10; SIGLEC11; SIGLEC12; SIGLEC14; SIGLEC15; SIGLEC6; SIGLEC7; SIGLEC8; SIGLEC9; SIRPA; SIRPB1; SIRPD; SIRPG; SISP1; SLAMF6; SLAMF7; TAPBPL; TCRA; TCRB; TIMD4; TRA@; TRAV20; TRBC1; TRBV19; TRBV3-1; TRBV5-4; TRBV7-2; TRDV2; TREM1; TREM2; TREML1; TREML2; TREML4; TRGV3; TRGV5; TRGV7; TRGV9; VCAM1; VCAN; VPREB1; VPREB3; VSIG1; VSIG2; VSIG4; VSIG9; VSTM1; VSTM2; VTCN1;
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Immunoglobulin V-set domain Provide feedback
This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.
Internal database links
|Similarity to PfamA using HHSearch:||ig I-set Ig_2 Ig_3|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR013106
The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulphide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains: alpha, delta, epsilon, gamma and mu, all consisting of a variable domain (VH) and three (in alpha, delta and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). Ig molecules are highly modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. The domains in Ig and Ig-like molecules are grouped into four types: V-set (variable; INTERPRO), C1-set (constant-1; INTERPRO), C2-set (constant-2; INTERPRO) and I-set (intermediate; INTERPRO) [PUBMED:9417933]. Structural studies have shown that these domains share a common core Greek-key beta-sandwich structure, with the types differing in the number of strands in the beta-sheets as well as in their sequence patterns [PUBMED:15327963, PUBMED:11377196].
Immunoglobulin-like domains that are related in both sequence and structure can be found in several diverse protein families. Ig-like domains are involved in a variety of functions, including cell-cell recognition, cell-surface receptors, muscle structure and the immune system [PUBMED:10698639].
This entry represents the V-set domains, which are Ig-like domains resembling the antibody variable domain. V-set domains are found in diverse protein families, including immunoglobulin light and heavy chains; in several T-cell receptors such as CD2 (Cluster of Differentiation 2), CD4, CD80, and CD86; in myelin membrane adhesion molecules; in junction adhesion molecules (JAM); in tyrosine-protein kinase receptors; and in the programmed cell death protein 1 (PD1).
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
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Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions. The superfamily can be divided into discrete structural sets, by the presence or absence of beta-strands in the structure and the length of the domains . Proteins containing domains of the C1 and V-sets are mostly molecules of the vertebrate immune system. Proteins of the C2-set are mainly lymphocyte antigens, this differs from the composition of the C2-set as originally proposed . The I-set is intermediate in structure between the C1 and V-sets and is found widely in cell surface proteins as well as intracellular muscle proteins.
The clan contains the following 24 members:A2M Adeno_E3_CR1 Adhes-Ig_like C1-set C2-set C2-set_2 Herpes_gE Herpes_gI Herpes_glycop_D I-set ICAM_N ig Ig_2 Ig_3 Ig_Tie2_1 IZUMO K1 Lep_receptor_Ig Marek_A PTCRA Receptor_2B4 SVA V-set V-set_CD47
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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Curation and family details
|Seed source:||Bateman A|
|Number in seed:||113|
|Number in full:||19537|
|Average length of the domain:||107.80 aa|
|Average identity of full alignment:||17 %|
|Average coverage of the sequence by the domain:||38.44 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||12|
|Download:||download the raw HMM for this family|
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The tree shows the occurrence of this domain across different species. More...
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There are 23 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the V-set domain has been found. There are 695 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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