Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
1  structure 140  species 0  interactions 3816  sequences 320  architectures

Family: VWC (PF00093)

Summary: von Willebrand factor type C domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Von Willebrand factor type C domain". More...

Von Willebrand factor type C domain Edit Wikipedia article


von Willebrand factor type C domain
Identifiers
Symbol VWC
Pfam PF00093
InterPro IPR001007

Von Willebrand factor, type C is a protein domain is found in various blood plasma proteins: complement factors B, C2, CR3 and CR4; the integrins (I-domains); collagen types VI, VII, XII and XIV; and other extracellular proteins.[1][2][3]

Contents

[edit] Function

Although the majority of VWA-containing proteins are extracellular, the most ancient ones present in all eukaryotes are all intracellular proteins involved in functions such as transcription, DNA repair, ribosomal and membrane transport and the proteasome.

A common feature appears to be involvement in multiprotein complexes. Proteins that incorporate vWF domains participate in numerous biological events (e.g. cell adhesion, migration, homing, pattern formation, and signal transduction), involving interaction with a large array of ligands.[1]

[edit] Mutation effects

A number of human diseases arise from mutations in VWA domains.[2]

The domain is named after the von Willebrand factor (VWF) type C repeat which is found in multidomain protein/multifunctional proteins involved in maintaining homeostasis.[3][4] For the von Willebrand factor the duplicated VWFC domain is thought to participate in oligomerization, but not in the initial dimerization step.[5] The presence of this region in a number of other complex-forming proteins points to the possible involvement of the VWFC domain in complex formation.

[edit] Human proteins containing this domain

BMPER; CHRD; CHRDL1; CHRDL2; COL1A1; COL2A1; COL3A1; COL5A2; CRIM1; CTGF; CYR61; ECM2; FKSG37; FRAS1; MUC2; MUC5B; NELL1; NELL2; NOV; PXDNL; SSPO; THBS1; THBS2; VWC2; VWCE; VWF; WISP1; WISP2;

[edit] References

  1. ^ a b Colombatti A, Bonaldo P, Doliana R (1993). "Type A modules: interacting domains found in several non-fibrillar collagens and in other extracellular matrix proteins". Matrix 13 (4): 297–306. doi:10.1016/S0934-8832(11)80025-9. PMID 8412987. 
  2. ^ a b Smith KF, Haris PI, Chapman D, Perkins SJ, Williams SC, Sim RB (1994). "The secondary structure of the von Willebrand factor type A domain in factor B of human complement by Fourier transform infrared spectroscopy. Its occurrence in collagen types VI, VII, XII and XIV, the integrins and other proteins by averaged structure predictions". J. Mol. Biol. 238 (1): 104–119. doi:10.1006/jmbi.1994.1271. PMID 8145250. 
  3. ^ a b Bork P (1991). "Shuffled domains in extracellular proteins". FEBS Lett. 286 (1): 47–54. doi:10.1016/0014-5793(91)80937-X. PMID 1864378. 
  4. ^ Hunt LT, Barker WC (1987). "von Willebrand factor shares a distinctive cysteine-rich domain with thrombospondin and procollagen". Biochem. Biophys. Res. Commun. 144 (2): 876–882. doi:10.1016/S0006-291X(87)80046-3. PMID 3495268. 
  5. ^ Voorberg J, Fontijn R, Calafat J, Janssen H, van Mourik JA, Pannekoek H (1991). "Assembly and routing of von Willebrand factor variants: the requirements for disulfide-linked dimerization reside within the carboxy-terminal 151 amino acids". J. Cell Biol. 113 (1): 195–205. doi:10.1083/jcb.113.1.195. PMC 2288914. PMID 2007623. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2288914. 

This article incorporates text from the public domain Pfam and InterPro IPR001007

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.

von Willebrand factor type C domain Provide feedback

The high cutoff was used to prevent overlap with PF00094.

Literature references

  1. Bork P; , FEBS Lett 1993;327:125-130.: The modular architecture of a new family of growth regulators related to connective tissue growth factor. PUBMED:7687569 EPMC:7687569


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001007

The vWF domain is found in various plasma proteins: complement factors B, C2, CR3 and CR4; the integrins (I-domains); collagen types VI, VII, XII and XIV; and other extracellular proteins [PUBMED:8412987, PUBMED:8145250, PUBMED:1864378]. Although the majority of VWA-containing proteins are extracellular, the most ancient ones present in all eukaryotes are all intracellular proteins involved in functions such as transcription, DNA repair, ribosomal and membrane transport and the proteasome. A common feature appears to be involvement in multiprotein complexes. Proteins that incorporate vWF domains participate in numerous biological events (e.g. cell adhesion, migration, homing, pattern formation, and signal transduction), involving interaction with a large array of ligands [PUBMED:8412987]. A number of human diseases arise from mutations in VWA domains. Secondary structure prediction from 75 aligned vWF sequences has revealed a largely alternating sequence of alpha-helices and beta-strands [PUBMED:8145250]. The domain is named after the von Willebrand factor (VWF) type C repeat which is found in multidomain protein/multifunctional proteins involved in maintaining homeostasis [PUBMED:3495268, PUBMED:1864378]. For the von Willebrand factor the duplicated VWFC domain is thought to participate in oligomerization, but not in the initial dimerization step [PUBMED:2007623]. The presence of this region in a number of other complex-forming proteins points to the possible involvment of the VWFC domain in complex formation.

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...

Loading domain graphics...

Pfam Clan

This family is a member of clan FnI-like (CL0451), which has the following description:

This superfamily is characterised by being disulfide-rich, all-beta with an extra C-terminal domain in the fibronectin-like, Fn1, members.

The clan contains the following 3 members:

PSP94 TILa VWC

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

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
(20)
Full
(3816)
Representative proteomes NCBI
(3212)
Meta
(3)
RP15
(372)
RP35
(529)
RP55
(1087)
RP75
(1998)
Jalview View  View  View  View  View  View  View  View 
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

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

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

Format an alignment

  Seed
(20)
Full
(3816)
Representative proteomes NCBI
(3212)
Meta
(3)
RP15
(372)
RP35
(529)
RP55
(1087)
RP75
(1998)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(20)
Full
(3816)
Representative proteomes NCBI
(3212)
Meta
(3)
RP15
(372)
RP35
(529)
RP55
(1087)
RP75
(1998)
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:

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: Published_alignment
Previous IDs: vwc;
Type: Family
Author: Sonnhammer ELL
Number in seed: 20
Number in full: 3816
Average length of the domain: 59.00 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 11.54 %

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 26.3 26.3
Trusted cut-off 26.3 26.3
Noise cut-off 26.2 26.2
Model length: 57
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 VWC domain has been found. There are 1 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...