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56  structures 68  species 4  interactions 320  sequences 44  architectures

Family: C2-set (PF05790)

Summary: Immunoglobulin C2-set domain

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This is the Wikipedia entry entitled "Immunoglobulin C2-set domain". More...

Immunoglobulin C2-set domain Edit Wikipedia article

Immunoglobulin C2-set domain
Identifiers
Symbol C2-set
Pfam PF05790
InterPro IPR008424

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; IPR013106), C1-set (constant-1; IPR003597), C2-set (constant-2; IPR008424) and I-set (intermediate; IPR013098).[1] 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.[2][3]

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.[4]

C2-set domains, which are Ig-like domains resembling the antibody constant domain. C2-set domains are found primarily in the mammalian T-cell surface antigens CD2 (Cluster of Differentiation 2), CD4 and CD80, as well as in vascular (VCAM) and intercellular (ICAM) cell adhesion molecules.

CD2 mediates T-cell adhesion via its ectodomain, and signal transduction utilising its 117-amino acid cytoplasmic tail.[5] CD2 displays structural and functional similarities with African swine fever virus (ASFV) LMW8-DR, a protein that is involved in cell–cell adhesion and immune response modulation, suggesting a possible role in the pathogenesis of ASFV infection.[6] CD4 is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence. Certain extracellular domains may be involved in dimerisation.[7]

References[edit]

  1. ^ Smith DK, Xue H (1997). "Sequence profiles of immunoglobulin and immunoglobulin-like domains". J. Mol. Biol. 274 (4): 530–545. doi:10.1006/jmbi.1997.1432. PMID 9417933. 
  2. ^ Potapov V, Sobolev V, Edelman M, Kister A, Gelfand I (2004). "Protein-Protein Recognition: Juxtaposition of Domain and Interface Cores in Immunoglobulins and Other Sandwich-like Proteins". J. Mol. Biol. 342 (2): 665–679. doi:10.1016/j.jmb.2004.06.072. PMID 15327963. 
  3. ^ Clarke J, Fowler SB (2001). "Mapping the folding pathway of an immunoglobulin domain: structural detail from Phi value analysis and movement of the transition state". Structure 9 (5): 355–366. doi:10.1016/S0969-2126(01)00596-2. PMID 11377196. 
  4. ^ Chothia C, Teichmann SA (2000). "Immunoglobulin superfamily proteins in Caenorhabditis elegans". J. Mol. Biol. 296 (5): –. doi:10.1006/jmbi.1999.3497. PMID 10698639. 
  5. ^ Reinherz EL, Yang H (2001). "Dynamic recruitment of human CD2 into lipid rafts. Linkage to T cell signal transduction". J. Biol. Chem. 276 (22): 18775–18785. doi:10.1074/jbc.M009852200. PMID 11376005. 
  6. ^ Kutish GF, Rock DL, Afonso CL, Borca MV, Irusta P, Carrillo C, Brun A, Sussman M (1994). "An African swine fever virus gene with similarity to the T-lymphocyte surface antigen CD2 mediates hemadsorption". Virology 199 (2): 463–468. doi:10.1006/viro.1994.1146. PMID 7907198. 
  7. ^ Sanejouand YH (2004). "Domain swapping of CD4 upon dimerization". Proteins 57 (1): –. doi:10.1002/prot.20197. PMID 15326605. 

Human proteins containing this domain[edit]

CD2; CD4; VCAM1;

References[edit]

This article incorporates text from the public domain Pfam and InterPro IPR008424


This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008424

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 C2-set domains, which are Ig-like domains resembling the antibody constant domain. C2-set domains are found primarily in the mammalian T-cell surface antigens CD2 (Cluster of Differentiation 2), CD4 and CD80, as well as in vascular (VCAM) and intercellular (ICAM) cell adhesion molecules.

CD2 mediates T-cell adhesion via its ectodomain, and signal transduction utilising its 117-amino acid cytoplasmic tail [PUBMED:11376005]. CD2 displays structural and functional similarities with African swine fever virus (ASFV) LMW8-DR, a protein that is involved in cell-cell adhesion and immune response modulation, suggesting a possible role in the pathogenesis of ASFV infection [PUBMED:7907198]. CD4 is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence. Certain extracellular domains may be involved in dimerisation [PUBMED:15326605].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Ig (CL0011), which has the following description:

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 [1]. 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 [1]. 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

Alignments

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(27)
Full
(320)
Representative proteomes NCBI
(345)
Meta
(1)
RP15
(5)
RP35
(5)
RP55
(12)
RP75
(79)
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Format an alignment

  Seed
(27)
Full
(320)
Representative proteomes NCBI
(345)
Meta
(1)
RP15
(5)
RP35
(5)
RP55
(12)
RP75
(79)
Alignment:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(27)
Full
(320)
Representative proteomes NCBI
(345)
Meta
(1)
RP15
(5)
RP35
(5)
RP55
(12)
RP75
(79)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Bateman A
Previous IDs: CD2;
Type: Domain
Author: Bateman A, Finn RD, Moxon SJ
Number in seed: 27
Number in full: 320
Average length of the domain: 77.80 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 27.95 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.3 21.3
Trusted cut-off 21.3 21.5
Noise cut-off 21.2 21.2
Model length: 80
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 4 interactions for this family. More...

I-set ig CD4-extracel C2-set

Structures

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 C2-set domain has been found. There are 56 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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