Summary: Collagen triple helix repeat (20 copies)
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This is the Wikipedia entry entitled "Collagen helix". More...
Collagen helix Edit Wikipedia article
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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.
Collagen triple helix repeat (20 copies) Provide feedback
Members of this family belong to the collagen superfamily [1]. Collagens are generally extracellular structural proteins involved in formation of connective tissue structure. The alignment contains 20 copies of the G-X-Y repeat that forms a triple helix. The first position of the repeat is glycine, the second and third positions can be any residue but are frequently proline and hydroxy-proline. Collagens are post translationally modified by proline hydroxylase to form the hydroxy-proline residues. Defective hydroxylation is the cause of scurvy. Some members of the collagen superfamily are not involved in connective tissue structure but share the same triple helical structure. The family includes bacterial collagen-like triple-helix repeat proteins [2,3].
Literature references
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Mayne R, Brewton RG; , Curr Opin Cell Biol 1993;5:883-890.: New members of the collagen superfamily PUBMED:8240831 EPMC:8240831
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Whatmore AM;, Microbiology. 2001;147:419-429.: Streptococcus pyogenes sclB encodes a putative hypervariable surface protein with a collagen-like repetitive structure. PUBMED:11158359 EPMC:11158359
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McElroy K, Mouton L, Du Pasquier L, Qi W, Ebert D;, Res Microbiol. 2011;162:701-714.: Characterisation of a large family of polymorphic collagen-like proteins in the endospore-forming bacterium Pasteuria ramosa. PUBMED:21726633 EPMC:21726633
Internal database links
SCOOP: | DUF4988 |
External database links
MIM: | 240400 |
SCOP: | 1a9a |
This tab holds annotation information from the InterPro database.
InterPro entry IPR008160
Members of this family belong to the collagen superfamily [PUBMED:8240831]. Collagens are generally extracellular structural proteins involved in formation of connective tissue structure. The sequence is predominantly repeats of the G-X-Y and the polypeptide chains form a triple helix. The first position of the repeat is glycine, the second and third positions can be any residue but are frequently proline and hydroxyproline. Collagens are post-translationally modified by proline hydroxylase to form the hydroxyproline residues. Defective hydroxylation is the cause of scurvy.
Some members of the collagen superfamily are not involved in connective tissue structure but share the same triple helical structure.
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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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 (41) |
Full (96356) |
Representative proteomes | UniProt (193914) |
NCBI (434268) |
Meta (5024) |
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RP15 (14424) |
RP35 (32760) |
RP55 (65390) |
RP75 (99854) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (41) |
Full (96356) |
Representative proteomes | UniProt (193914) |
NCBI (434268) |
Meta (5024) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (14424) |
RP35 (32760) |
RP55 (65390) |
RP75 (99854) |
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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.
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
Seed source: | Swissprot |
Previous IDs: | none |
Type: | Repeat |
Sequence Ontology: | SO:0001068 |
Author: |
Bateman A |
Number in seed: | 41 |
Number in full: | 96356 |
Average length of the domain: | 62.60 aa |
Average identity of full alignment: | 40 % |
Average coverage of the sequence by the domain: | 29.58 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 60 | ||||||||||||
Family (HMM) version: | 19 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 13 interactions for this family. More...
V-set Surfac_D-trimer Peptidase_M10 Fibrinogen_C Surfac_D-trimer Kazal_1 Collagen_bind Hemopexin SPARC_Ca_bdg fn1 Collagen C1q Fibritin_CStructures
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 Collagen domain has been found. There are 322 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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