Summary: Integrin beta chain VWA domain
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This is the Wikipedia entry entitled "Integrin". More...
Integrin Edit Wikipedia article
An integrin, or integrin receptor, is a receptor in the plasma membrane of biological cells. Integrins play an important role in:
- Integration of the cell into the surrounding tissue by
- cell-cell-interaction
- adhesive interaction
- Embryonal development
- Tumor development
- Apoptosis
- Connection between intracellular and extracellular scaffolding
Among the ligands of integrins are fibronectin and collagen, both part of the extracellular matrix. Ligand binding leads to clustering (cross-connection) of the multivalent components of the integrin to a functional protein complex. Integrins have no intrinsic kinase activity, but associate kinases (for example, focal adhesion kinase, FAK) on the cytoplasmic side of the membrane.
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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.
Integrin beta chain VWA domain Provide feedback
Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer [1]. This domain corresponds to the integrin beta VWA domain.
Literature references
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May AP, Ponting CP; , Trends Biochem Sci 1999;24:12-13.: Integrin alpha- and beta 4-subunit-domain homologues in cyanobacterial proteins. PUBMED:10087915 EPMC:10087915
Internal database links
SCOOP: | VWA VWA_2 |
External database links
PROSITE: | PDOC00216 |
SCOP: | 1jv2 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR002369
Integrins are the major metazoan receptors for cell adhesion to extracellular matrix proteins and, in vertebrates, also play important roles in certain cell-cell adhesions, make transmembrane connections to the cytoskeleton and activate many intracellular signalling pathways [ PUBMED:12297042 , PUBMED:12361595 ]. An integrin receptor is a heterodimer composed of alpha and beta subunits. Each subunit crosses the membrane once, with most of the polypeptide residing in the extracellular space, and has two short cytoplasmic domains. Some members of this family have EGF repeats at the C terminus and also have a vWA domain inserted within the integrin domain at the N terminus.
Most integrins recognise relatively short peptide motifs, and in general require an acidic amino acid to be present. Ligand specificity depends upon both the alpha and beta subunits [ PUBMED:12234368 ]. There are at least 18 types of alpha and 8 types of beta subunits recognised in humans [ PUBMED:14689578 ]. Each alpha subunit tends to associate only with one type of beta subunit, but there are exceptions to this rule [ PUBMED:2467745 ]. Each association of alpha and beta subunits has its own binding specificity and signalling properties. Many integrins require activation on the cell surface before they can bind ligands. Integrins frequently intercommunicate, and binding at one integrin receptor activate or inhibit another.
Integrins are important therapeutic targets in conditions such as atherosclerosis, thrombosis, cancer and asthma [ PUBMED:2199285 ].
At the N terminus of the beta subunit is a cysteine-containing domain reminiscent of that found in presenillins and semaphorins, which has hence been termed the PSI domain. C-terminal to the PSI domain is an A-domain, which has been predicted to adopt a Rossmann fold similar to that of the alpha subunit, but with additional loops between the second and third beta strands [ PUBMED:9009218 ]. The murine gene Pactolus shares significant similarity with the beta subunit [ PUBMED:9535848 ], but lacks either one or both of the inserted loops. The C-terminal portion of the beta subunit extracellular domain contains an internally disulphide-bonded cysteine-rich region, while the intracellular tail contains putative sites of interaction with a variety of intracellular signalling and cytoskeletal proteins, such as focal adhesion kinase and alpha-actinin respectively [ PUBMED:9818167 ]. Integrin cytoplasmic domains are normally less than 50 amino acids in length, with the beta-subunit sequences exhibiting greater homology to each other than the alpha-subunit sequences. This is consistent with current evidence that the beta subunit is the principal site for binding of cytoskeletal and signalling molecules, whereas the alpha subunit has a regulatory role. The first 20 amino acids of the beta-subunit cytoplasmic domain are also alpha helical, but the final 25 residues are disordered and, apart from a turn that follows a conserved NPxY motif, appear to lack defined structure, suggesting that this is adopted on effector binding. The two membrane-proximal helices mediate the link between the subunits via a series of hydrophobic and electrostatic contacts.
This domain corresponds to the integrin beta VWA domain.
Domain organisation
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Pfam Clan
Alignments
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Seed (109) |
Full (5488) |
Representative proteomes | UniProt (8954) |
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RP15 (596) |
RP35 (1502) |
RP55 (4129) |
RP75 (5552) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (109) |
Full (5488) |
Representative proteomes | UniProt (8954) |
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RP15 (596) |
RP35 (1502) |
RP55 (4129) |
RP75 (5552) |
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Raw Stockholm | |||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full 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
Seed source: | Bateman A |
Previous IDs: | integrin_B; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 109 |
Number in full: | 5488 |
Average length of the domain: | 229.6 aa |
Average identity of full alignment: | 50 % |
Average coverage of the sequence by the domain: | 27.66 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 248 | ||||||||||||
Family (HMM) version: | 21 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 Integrin_beta domain has been found. There are 140 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 sequence.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.