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29  structures 126  species 1  interaction 3971  sequences 376  architectures

Family: C2-set_2 (PF08205)

Summary: CD80-like C2-set immunoglobulin 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]

[edit] References

  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.

[edit] Human proteins containing this domain

CD2; CD4; VCAM1;

[edit] References

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.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

CD80-like C2-set immunoglobulin domain Provide feedback

These domains belong to the immunoglobulin superfamily.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013162

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 C2-set type domains found in the T-cell antigen CD80, as well as in related proteins. CD80 (B7-1) is a glycoprotein expressed on antigen-presenting cells [PUBMED:10661405]. The shared ligands on CD80 and CD86 (B7-2) deliver the co-stimulatory signal through CD28 and CTLA-4 on T-cells, where CD28 augments the T-cell response and CTLA-4 attenuates it [PUBMED:11279502].

Domain organisation

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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
(33)
Full
(3971)
Representative proteomes NCBI
(9868)
Meta
(2)
RP15
(644)
RP35
(828)
RP55
(1357)
RP75
(2150)
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  Seed
(33)
Full
(3971)
Representative proteomes NCBI
(9868)
Meta
(2)
RP15
(644)
RP35
(828)
RP55
(1357)
RP75
(2150)
Alignment:
Format:
Order:
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
(33)
Full
(3971)
Representative proteomes NCBI
(9868)
Meta
(2)
RP15
(644)
RP35
(828)
RP55
(1357)
RP75
(2150)
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.

Pfam alignments:

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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

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Curation View help on the curation process

Seed source: Pfam-B_280 (release 17.0)
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 33
Number in full: 3971
Average length of the domain: 86.30 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 19.89 %

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 20.8 20.8
Trusted cut-off 20.8 20.8
Noise cut-off 20.7 20.7
Model length: 89
Family (HMM) version: 7
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Species distribution

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Interactions

There is 1 interaction for this family. More...

V-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_2 domain has been found. There are 29 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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