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8  structures 325  species 0  interactions 1878  sequences 79  architectures

Family: RWD (PF05773)

Summary: RWD domain

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

RWD domain Provide feedback

This domain was identified in WD40 repeat proteins and Ring finger domain proteins [1]. The function of this domain is unknown. GCN2 is the alpha-subunit of the only translation initiation factor (eIF2 alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain [1] after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases. The structure forms an alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices [2].

Literature references

  1. Doerks T, Copley RR, Schultz J, Ponting CP, Bork P; , Genome Res 2002;12:47-56.: Systematic identification of novel protein domain families associated with nuclear functions. PUBMED:11779830 EPMC:11779830

  2. Nameki N, Yoneyama M, Koshiba S, Tochio N, Inoue M, Seki E, Matsuda T, Tomo Y, Harada T, Saito K, Kobayashi N, Yabuki T, Aoki M, Nunokawa E, Matsuda N, Sakagami N, Terada T, Shirouzu M, Yoshida M, Hirota H, Osanai T, Tanaka A, Arakawa T, Carninci P, Kawai, Protein Sci 2004;13:2089-2100.: Solution structure of the RWD domain of the mouse GCN2 protein. PUBMED:15273307 EPMC:15273307


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006575

The RWD eukaryotic domain is found in RING finger (INTERPRO) and WD repeat (INTERPRO) containing proteins and DEXDc-like helicase (INTERPRO) subfamily related to the ubiquitin-conjugating enzymes domain (INTERPRO).

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...

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Pfam Clan

This family is a member of clan UBC (CL0208), which has the following description:

This superfamily includes a diverse set of proteins that bind to ubiquitin [1].

The clan contains the following 9 members:

Prok-E2_A Prok-E2_B Prok-E2_C Prok-E2_D Prok-E2_E RWD UEV UFC1 UQ_con

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
(119)
Full
(1878)
Representative proteomes NCBI
(2204)
Meta
(23)
RP15
(383)
RP35
(606)
RP55
(961)
RP75
(1276)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(119)
Full
(1878)
Representative proteomes NCBI
(2204)
Meta
(23)
RP15
(383)
RP35
(606)
RP55
(961)
RP75
(1276)
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
(119)
Full
(1878)
Representative proteomes NCBI
(2204)
Meta
(23)
RP15
(383)
RP35
(606)
RP55
(961)
RP75
(1276)
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.

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: Pfam-B_3991 (release 8.0)
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 119
Number in full: 1878
Average length of the domain: 119.30 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 19.67 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.8 20.8
Trusted cut-off 20.8 20.8
Noise cut-off 20.7 20.7
Model length: 113
Family (HMM) version: 17
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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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 RWD domain has been found. There are 8 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.

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