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125  structures 367  species 7  interactions 2644  sequences 161  architectures

Family: Integrin_beta (PF00362)

Summary: Integrin beta chain VWA domain

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This is the Wikipedia entry entitled "Integrin". More...

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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

  1. 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

External database links

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

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 vWA-like (CL0128), which has the following description:

To add.

The clan contains the following 18 members:

CobT_C Copine DUF1194 DUF2201 DUF444 DUF58 Integrin_beta Ku_N Med25_VWA Sec23_trunk Ssl1 Ste5_C Tfb4 VWA vWA-TerF-like VWA_2 VWA_3 VWA_CoxE

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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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
(123)
Full
(2644)
Representative proteomes UniProt
(4700)
NCBI
(6935)
Meta
(2)
RP15
(316)
RP35
(817)
RP55
(1897)
RP75
(2833)
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PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(123)
Full
(2644)
Representative proteomes UniProt
(4700)
NCBI
(6935)
Meta
(2)
RP15
(316)
RP35
(817)
RP55
(1897)
RP75
(2833)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(123)
Full
(2644)
Representative proteomes UniProt
(4700)
NCBI
(6935)
Meta
(2)
RP15
(316)
RP35
(817)
RP55
(1897)
RP75
(2833)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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.

Note: You can also download the data file for the tree.

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: integrin_B;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Bateman A
Number in seed: 123
Number in full: 2644
Average length of the domain: 229.00 aa
Average identity of full alignment: 48 %
Average coverage of the sequence by the domain: 28.03 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.8 24.8
Trusted cut-off 24.8 24.8
Noise cut-off 24.7 24.3
Model length: 248
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Interactions

There are 7 interactions for this family. More...

VWA MHC_II_alpha Integrin_alpha2 MHC_II_beta Integrin_B_tail FG-GAP Integrin_beta

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 125 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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