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19  structures 1524  species 0  interactions 9850  sequences 267  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

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006575

The RWD domain is a conserved region of about 110 amino acid residues, which has been identified in the mouse GCN2 eIF2alpha kinase and histidyl-tRNA synthetase and in presumed orthologues in other eukaryotic species from yeast to vertebrates. Additionally, it is also found in WD repeat containing proteins, yeast DEAD (DEXD)-like helicases, many RING-finger containing proteins, the UPF0029 uncharacterised protein family and a range of hypothetical proteins. The RWD domain has been named after the better characterised RING finger and WD repeat containing proteins and DEAD-like helicases. It has been proposed that the RWD domain might have a function in protein interaction [ PUBMED:11779830 ].

The RWD domain is predicted to have an alpha/beta secondary structure and is thought to be related to ubiquitin-conjugating enzymes (UBCc) domain, although the catalytic cysteine critical for ubiquitin-conjugating activity is not conserved in most members of the novel subfamily [ PUBMED:11779830 ].

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 14 members:

E2-ntca FANCL_d1 FANCL_d2 FANCL_d3 Knl1_RWD_C Prok-E2_A Prok-E2_B Prok-E2_C Prok-E2_D Prok-E2_E RWD UEV UFC1 UQ_con


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.

Representative proteomes UniProt
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PP/heatmap 1            

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

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

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Representative proteomes UniProt

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.

Representative proteomes UniProt
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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...


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
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 114
Number in full: 9850
Average length of the domain: 117.1 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 17.88 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.8 22.8
Trusted cut-off 22.8 22.8
Noise cut-off 22.7 22.7
Model length: 116
Family (HMM) version: 25
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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


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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 19 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
A0A044RAN6 View 3D Structure Click here
A0A044SVI6 View 3D Structure Click here
A0A044SXE6 View 3D Structure Click here
A0A044V255 View 3D Structure Click here
A0A044V734 View 3D Structure Click here
A0A044V9V0 View 3D Structure Click here
A0A077YY72 View 3D Structure Click here
A0A077Z1E7 View 3D Structure Click here
A0A077ZI62 View 3D Structure Click here
A0A0B4KHX7 View 3D Structure Click here
A0A0D2DNQ8 View 3D Structure Click here
A0A0D2ENY3 View 3D Structure Click here
A0A0D2F6Q2 View 3D Structure Click here
A0A0D2GXD8 View 3D Structure Click here
A0A0D2H4M9 View 3D Structure Click here
A0A0G2JZH9 View 3D Structure Click here
A0A0H5RZA9 View 3D Structure Click here
A0A0I9NBC8 View 3D Structure Click here
A0A0J9Y1S2 View 3D Structure Click here
A0A0K0E7H7 View 3D Structure Click here
A0A0K0ER64 View 3D Structure Click here
A0A0K0JET8 View 3D Structure Click here
A0A0N4U7G4 View 3D Structure Click here
A0A0N4UDE8 View 3D Structure Click here
A0A0N4UGT9 View 3D Structure Click here
A0A0N4UKM6 View 3D Structure Click here
A0A0P0VN75 View 3D Structure Click here
A0A0P0WE82 View 3D Structure Click here
A0A0R0IY34 View 3D Structure Click here
A0A0R0L574 View 3D Structure Click here
A0A158Q643 View 3D Structure Click here
A0A175VSV6 View 3D Structure Click here
A0A175W4R1 View 3D Structure Click here
A0A175W717 View 3D Structure Click here
A0A175WD74 View 3D Structure Click here
A0A1C1C8S6 View 3D Structure Click here
A0A1C1CB17 View 3D Structure Click here
A0A1C1CB46 View 3D Structure Click here
A0A1C1CPU1 View 3D Structure Click here
A0A1C1CTQ4 View 3D Structure Click here