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5  structures 1046  species 0  interactions 1372  sequences 8  architectures

Family: DUF2205 (PF10224)

Summary: Short coiled-coil protein

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 "Domain of unknown function". More...

Domain of unknown function Edit Wikipedia article

A Domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF188 and DUF1000. There are now over 3,000 DUF families within the Pfam database representing over 20% of known families.

History

The DUF naming scheme was introduced by Chris Ponting, through the addition of DUF1 and DUF2 to the SMART database.[1] These two domains were found to be widely distributed in bacterial signaling proteins. Subsequently, the functions of these domains were identified and they have since been renamed as the GGDEF domain and EAL domain respectively.

Structure

Structural genomics programmes have attempted to understand the function of DUFs through structure determination. The structures of over 250 DUF families have been solved.[2]

External Links

List of Pfam familes beginning with the letter D, including DUF families

References

  1. ^ Schultz J, Milpetz F, Bork P, Ponting CP (1998). "SMART, a simple modular architecture research tool: identification of signaling domains". Proc. Natl. Acad. Sci. U.S.A. 95 (11): 5857–64. PMC 34487. PMID 9600884. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  2. ^ Jaroszewski L, Li Z, Krishna SS; et al. (2009). "Exploration of uncharted regions of the protein universe". PLoS Biol. 7 (9): e1000205. doi:10.1371/journal.pbio.1000205. PMC 2744874. PMID 19787035. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

"DUF" families are annotated with the Domain of unknown function Wikipedia article. This is a general article, with no specific information about individual Pfam DUFs. If you have information about this particular DUF, please let us know using the "Add annotation" button below.

Short coiled-coil protein Provide feedback

This entry represents a highly conserved 100 residue coiled-coil region which is found in short coiled-coil protein (SCOC) in human and UNC-69 in Caenorhabditis elegans. In human, SCOC is required for autophagosome formation during amino acid starvation. It forms a starvation-sensitive trimeric complex with UVRAG (UV radiation resistance associated gene) and FEZ1 and may regulate ULK1 and Beclin 1 complex activities [1]. In C. elegans, this small, evolutionarily conserved coiled-coil domain-containing protein, UNC-69, acts as a binding partner of UNC-76. Together they participate in a common genetic pathway necessary for axon extension and cooperate to regulate the size and position of synaptic vesicles in axons. Moreover, both proteins colocalize as puncta in neuronal processes and mutations in UNC-69 preferentially disrupt membrane traffic within axons [2].

Literature references

  1. McKnight NC, Jefferies HB, Alemu EA, Saunders RE, Howell M, Johansen T, Tooze SA;, EMBO J. 2012;31:1931-1946.: Genome-wide siRNA screen reveals amino acid starvation-induced autophagy requires SCOC and WAC. PUBMED:22354037 EPMC:22354037

  2. Su CW, Tharin S, Jin Y, Wightman B, Spector M, Meili D, Tsung N, Rhiner C, Bourikas D, Stoeckli E, Garriga G, Horvitz HR, Hengartner MO;, J Biol. 2006;5:9.: The short coiled-coil domain-containing protein UNC-69 cooperates with UNC-76 to regulate axonal outgrowth and normal presynaptic organization in Caenorhabditis elegans. PUBMED:16725058 EPMC:16725058


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR019357

This entry represents short coiled-coil protein (SCOC). In human, SCOC is required for autophagosome formation during amino acid starvation. It forms a starvation-sensitive trimeric complex with UVRAG (UV radiation resistance associated gene) and FEZ1 and may regulate ULK1 and Beclin 1 complex activities [ PUBMED:22354037 ].

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
(21)
Full
(1372)
Representative proteomes UniProt
(2270)
RP15
(235)
RP35
(541)
RP55
(997)
RP75
(1386)
Jalview View  View  View  View  View  View  View 
HTML View  View           
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
(21)
Full
(1372)
Representative proteomes UniProt
(2270)
RP15
(235)
RP35
(541)
RP55
(997)
RP75
(1386)
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
(21)
Full
(1372)
Representative proteomes UniProt
(2270)
RP15
(235)
RP35
(541)
RP55
(997)
RP75
(1386)
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: KOGs (KOG3650)
Previous IDs: none
Type: Coiled-coil
Sequence Ontology: SO:0001080
Author: El-Gebali S , KOGs, Finn RD , Coggill P
Number in seed: 21
Number in full: 1372
Average length of the domain: 73 aa
Average identity of full alignment: 44 %
Average coverage of the sequence by the domain: 54.87 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.7 26.7
Trusted cut-off 27.1 26.9
Noise cut-off 26.4 26.5
Model length: 75
Family (HMM) version: 12
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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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 DUF2205 domain has been found. There are 5 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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