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374  structures 2373  species 0  interactions 122961  sequences 1977  architectures

Family: Collagen (PF01391)

Summary: Collagen triple helix repeat (20 copies)

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 "Collagen helix". More...

Collagen helix Edit Wikipedia article

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.

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

  1. Mayne R, Brewton RG; , Curr Opin Cell Biol 1993;5:883-890.: New members of the collagen superfamily PUBMED:8240831 EPMC:8240831

  2. 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

  3. 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

External database links

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 and the UniProtKB 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
(41)
Full
(122961)
Representative proteomes UniProt
(243459)
RP15
(19977)
RP35
(48105)
RP55
(109158)
RP75
(147047)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(41)
Full
(122961)
Representative proteomes UniProt
(243459)
RP15
(19977)
RP35
(48105)
RP55
(109158)
RP75
(147047)
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
(41)
Full
(122961)
Representative proteomes UniProt
(243459)
RP15
(19977)
RP35
(48105)
RP55
(109158)
RP75
(147047)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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: Swissprot
Previous IDs: none
Type: Repeat
Sequence Ontology: SO:0001068
Author: Bateman A , Eddy SR
Number in seed: 41
Number in full: 122961
Average length of the domain: 62.50 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 29.02 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.2 27.2
Trusted cut-off 27.2 27.2
Noise cut-off 27.1 27.1
Model length: 60
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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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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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 Collagen domain has been found. There are 374 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.

Protein Predicted structure External Information
A0A0G2JTX7 View 3D Structure Click here
A0A0G2JV12 View 3D Structure Click here
A0A0G2JV12 View 3D Structure Click here
A0A0G2JV12 View 3D Structure Click here
A0A0G2JV12 View 3D Structure Click here
A0A0G2K2Q8 View 3D Structure Click here
A0A0G2K2Q8 View 3D Structure Click here
A0A0G2K2Q8 View 3D Structure Click here
A0A0G2K2Q8 View 3D Structure Click here
A0A0G2K2Q8 View 3D Structure Click here
A0A0G2K2Q8 View 3D Structure Click here
A0A0G2K2Q8 View 3D Structure Click here
A0A0G2K2Q8 View 3D Structure Click here
A0A0G2K449 View 3D Structure Click here
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A0A0G2K601 View 3D Structure Click here
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A0A0G2K601 View 3D Structure Click here
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A0A0G2K742 View 3D Structure Click here
A0A0G2K742 View 3D Structure Click here
A0A0G2K742 View 3D Structure Click here
A0A0G2K742 View 3D Structure Click here
A0A0G2K742 View 3D Structure Click here
A0A0G2K742 View 3D Structure Click here
A0A0G2K742 View 3D Structure Click here
A0A0G2K742 View 3D Structure Click here
A0A0G2K742 View 3D Structure Click here
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A0A0G2K742 View 3D Structure Click here
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A0A0G2K742 View 3D Structure Click here
A0A0G2K742 View 3D Structure Click here
A0A0G2K742 View 3D Structure Click here
A0A0G2K7A5 View 3D Structure Click here
A0A0G2K7A5 View 3D Structure Click here
A0A0G2KCR2 View 3D Structure Click here
A0A0G2KMC2 View 3D Structure Click here
A0A0G2KMC2 View 3D Structure Click here
A0A0G2L8G8 View 3D Structure Click here
A0A0G2L8G8 View 3D Structure Click here
A0A0G2L8G8 View 3D Structure Click here
A0A0G2L8G8 View 3D Structure Click here
A0A0G2L8G8 View 3D Structure Click here
A0A0G2QC08 View 3D Structure Click here
A0A0G2QC08 View 3D Structure Click here
A0A0H2UKP2 View 3D Structure Click here
A0A0H2UKP2 View 3D Structure Click here
A0A0H2UKP2 View 3D Structure Click here
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A0A0H2UKP2 View 3D Structure Click here
A0A0H2UKP2 View 3D Structure Click here
A0A0H2UKP2 View 3D Structure Click here
A0A0H2UKP2 View 3D Structure Click here
A0A0H2UKP2 View 3D Structure Click here
A0A0H2UKP2 View 3D Structure Click here
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A0A0H2UKP2 View 3D Structure Click here
A0A0H2UKP2 View 3D Structure Click here
A0A0H2UKP2 View 3D Structure Click here
A0A0H2UKU2 View 3D Structure Click here
A0A0H2UKU2 View 3D Structure Click here
A0A0H2UKU2 View 3D Structure Click here
A0A0H2UKU2 View 3D Structure Click here
A0A0H2UKU2 View 3D Structure Click here
A0A0H2UKU2 View 3D Structure Click here
A0A0R4IAT5 View 3D Structure Click here
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A0A0R4IAT5 View 3D Structure Click here
A0A0R4ILV8 View 3D Structure Click here
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A0A0R4IN07 View 3D Structure Click here
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A0A0R4IRG2 View 3D Structure Click here
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A0A0R4IRG2 View 3D Structure Click here
A0A0R4IRG2 View 3D Structure Click here
A0A0R4IRN4 View 3D Structure Click here
A0A0R4IRN4 View 3D Structure Click here
A0A0R4ITJ5 View 3D Structure Click here
A0A0R4ITJ5 View 3D Structure Click here
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A0A0R4IW47 View 3D Structure Click here
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A0A140UHW8 View 3D Structure Click here
A0A286Y830 View 3D Structure Click here
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A0A286YAI0 View 3D Structure Click here
A0A2R8PXW9 View 3D Structure Click here
A0A2R8Q0C8 View 3D Structure Click here
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A0A2R8Q0C8 View 3D Structure Click here
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A0A2R8Q0C8 View 3D Structure Click here
A0A2R8Q1H3 View 3D Structure Click here
A0A2R8QBY7 View 3D Structure Click here
A0A2R8QCC1 View 3D Structure Click here
A0A2R8QCC1 View 3D Structure Click here
A0A2R8QCC1 View 3D Structure Click here
A0A2R8QCC1 View 3D Structure Click here
A0A2R8QES2 View 3D Structure Click here
A0A2R8QES2 View 3D Structure Click here
A0A2R8QES2 View 3D Structure Click here
A0A2R8QES2 View 3D Structure Click here
A0A2R8QES2 View 3D Structure Click here
A0A2R8QES2 View 3D Structure Click here
A0A2R8QES2 View 3D Structure Click here
A0A2R8QES2 View 3D Structure Click here
A0A2R8QES2 View 3D Structure Click here
A0A2R8QSK3 View 3D Structure Click here
A0A2R8QSK3 View 3D Structure Click here
A0A2R8QSK3 View 3D Structure Click here
A0A2R8QSK3 View 3D Structure Click here
A0A2R8QSK3 View 3D Structure Click here
A0A2R8QSK3 View 3D Structure Click here
A0A2R8QSK3 View 3D Structure Click here
A0A2R8RP31 View 3D Structure Click here
A0A2R8RP31 View 3D Structure Click here
A0A2R8RP31 View 3D Structure Click here
A0A2R8RP31 View 3D Structure Click here
A0A2R8RP31 View 3D Structure Click here
A0A2R8RPE2 View 3D Structure Click here
A0MSJ1 View 3D Structure Click here
A0MSJ1 View 3D Structure Click here
A0MSJ1 View 3D Structure Click here
A0MSJ1 View 3D Structure Click here
A0MSJ1 View 3D Structure Click here
A0MSJ1 View 3D Structure Click here
A0MSJ1 View 3D Structure Click here
A2ACT7 View 3D Structure Click here
A2ACT7 View 3D Structure Click here
A2ACT7 View 3D Structure Click here
A2ACT7 View 3D Structure Click here
A2ACT7 View 3D Structure Click here
A2ACT7 View 3D Structure Click here
A2AX52 View 3D Structure Click here
A3QM98 View 3D Structure Click here
A3QM98 View 3D Structure Click here
A5JYR8 View 3D Structure Click here
A5JYR8 View 3D Structure Click here
A5JYR8 View 3D Structure Click here
A5PMY6 View 3D Structure Click here
A5PMY6 View 3D Structure Click here
A5PMY6 View 3D Structure Click here
A5PN28 View 3D Structure Click here
A5PN28 View 3D Structure Click here
A5WW97 View 3D Structure Click here
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A5WW97 View 3D Structure Click here
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A5WWD4 View 3D Structure Click here
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A6H584 View 3D Structure Click here
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A6NHN0 View 3D Structure Click here
A6NHN0 View 3D Structure Click here
A6NHN0 View 3D Structure Click here
A6NHN0 View 3D Structure Click here
A6NMZ7 View 3D Structure Click here
A8TX70 View 3D Structure Click here
A8TX70 View 3D Structure Click here
A8TX70 View 3D Structure Click here
A8TX70 View 3D Structure Click here
A8WGB1 View 3D Structure Click here
B0S5W0 View 3D Structure Click here
B0S5W0 View 3D Structure Click here
B0S5W0 View 3D Structure Click here
B0S5W0 View 3D Structure Click here
B0S8G4 View 3D Structure Click here
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B0UXF7 View 3D Structure Click here
B0UXF7 View 3D Structure Click here
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B0UXF7 View 3D Structure Click here
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B0UXF7 View 3D Structure Click here
B0UXF7 View 3D Structure Click here
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B0UYF9 View 3D Structure Click here
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B1AVK5 View 3D Structure Click here
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B1AVK5 View 3D Structure Click here
B1WC91 View 3D Structure Click here
B2RNN3 View 3D Structure Click here
B7Z0K8 View 3D Structure Click here
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B8A4S4 View 3D Structure Click here
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C0H5W1 View 3D Structure Click here
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C0H5W1 View 3D Structure Click here
C7DZK3 View 3D Structure Click here
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C7DZK3 View 3D Structure Click here
C7DZK3 View 3D Structure Click here
C7DZK3 View 3D Structure Click here
D3Z9E1 View 3D Structure Click here
D3ZCQ0 View 3D Structure Click here
D3ZCQ0 View 3D Structure Click here
D3ZCQ0 View 3D Structure Click here
D3ZCQ0 View 3D Structure Click here
D3ZCQ0 View 3D Structure Click here
D3ZCQ0 View 3D Structure Click here
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D3ZCS2 View 3D Structure Click here
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D3ZDS2 View 3D Structure Click here
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D3ZE04 View 3D Structure Click here
D3ZE04 View 3D Structure Click here
D3ZE04 View 3D Structure Click here
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D3ZE04 View 3D Structure Click here
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D3ZE04 View 3D Structure Click here
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D3ZEN8 View 3D Structure Click here
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D3ZL10 View 3D Structure Click here
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D3ZN64 View 3D Structure Click here
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D3ZPA7 View 3D Structure Click here
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D3ZX71 View 3D Structure Click here
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D3ZZT9 View 3D Structure Click here
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D4A213 View 3D Structure Click here
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