Summary: CD80-like C2-set immunoglobulin domain
This is the Wikipedia entry entitled "Immunoglobulin C2-set domain". More...
The Wikipedia text that you see displayed here is a download from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button next to the article title ("Edit Wikipedia article") takes you to the edit page for the article directly within Wikipedia. You should be aware you are not editing our local copy of this information. Any changes that you make to the Wikipedia article will not be displayed here until we next download the article from Wikipedia. We currently download new content on a nightly basis.
Does Pfam agree with the content of the Wikipedia entry ?
Pfam has chosen to link families to Wikipedia articles. In some case we have created or edited these articles but in many other cases we have not made any direct contribution to the content of the article. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Pfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.
Editing Wikipedia articles
Before you edit for the first time
Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.
You should take a few minutes to view the following pages:
How your contribution will be recorded
Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia article" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer's IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.
If you have problems editing a particular page, contact us at firstname.lastname@example.org and we will try to help.
The community annotation is a new facility of the Pfam web site. If you have problems editing or experience problems with these pages please contact us.
Immunoglobulin C2-set domain Edit Wikipedia article
|Immunoglobulin C2-set domain|
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). 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.
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 cellâcell recognition, cell-surface receptors, muscle structure and the immune system.
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. CD2 displays structural and functional similarities with African swine fever virus (ASFV) LMW8-DR, a protein that is involved in cellâcell adhesion and immune response modulation, suggesting a possible role in the pathogenesis of ASFV infection. 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.
- Smith DK, Xue H (1997). "Sequence profiles of immunoglobulin and immunoglobulin-like domains". J. Mol. Biol. 274 (4): 530â545. doi:10.1006/jmbi.1997.1432. PMID 9417933.
- 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): 665â679. doi:10.1016/j.jmb.2004.06.072. PMID 15327963.
- 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): 355â366. doi:10.1016/S0969-2126(01)00596-2. PMID 11377196.
- Chothia C, Teichmann SA (2000). "Immunoglobulin superfamily proteins in Caenorhabditis elegans". J. Mol. Biol. 296 (5): -. doi:10.1006/jmbi.1999.3497. PMID 10698639.
- Reinherz EL, Yang H (2001). "Dynamic recruitment of human CD2 into lipid rafts. Linkage to T cell signal transduction". J. Biol. Chem. 276 (22): 18775â18785. doi:10.1074/jbc.M009852200. PMID 11376005.
- 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): 463â468. doi:10.1006/viro.1994.1146. PMID 7907198.
- Sanejouand YH (2004). "Domain swapping of CD4 upon dimerization". Proteins 57 (1): -. doi:10.1002/prot.20197. PMID 15326605.
 Human proteins containing this domain
|This membrane protein-related article is a stub. You can help Wikipedia by expanding it.|
CD80-like C2-set immunoglobulin domain Provide feedback
These domains belong to the immunoglobulin superfamily.
Internal database links
|Similarity to PfamA using HHSearch:||ig Marek_A C1-set I-set Ig_2 Ig_3|
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].
- 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.
Loading domain graphics...
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:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Seed source:||Pfam-B_280 (release 17.0)|
|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 build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||7|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
There is 1 interaction 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 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.
Loading structure mapping...