Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
49  structures 1231  species 0  interactions 24686  sequences 567  architectures

Family: RA (PF00788)

Summary: Ras association (RalGDS/AF-6) domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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.

Ras association (RalGDS/AF-6) domain Provide feedback

RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Recent evidence (not yet in MEDLINE) shows that some RA domains do NOT bind RasGTP. Predicted structure [3] similar to that determined [1] and that of the RasGTP-binding domain of Raf kinase.

Literature references

  1. Huang L, Weng X, Hofer F, Martin GS, Kim SH; , Nat Struct Biol 1997;4:609-615.: Three-dimensional structure of the Ras-interacting domain of RalGDS. PUBMED:9253406 EPMC:9253406

  2. Hofer F, Fields S, Schneider C, Martin GS; , Proc Natl Acad Sci U S A 1994;91:11089-11093.: Activated Ras interacts with the Ral guanine nucleotide dissociation stimulator. PUBMED:7972015 EPMC:7972015

  3. Ponting CP, Benjamin DR; , Trends Biochem Sci 1996;21:422-425.: A novel family of Ras-binding domains. PUBMED:8987396 EPMC:8987396

  4. Kuriyama M, Harada N, Kuroda S, Yamamoto T, Nakafuku M, Iwamatsu A, Yamamoto D, Prasad R, Croce C, Canaani E, Kaibuchi K; , J Biol Chem 1996;271:607-610.: Identification of AF-6 and canoe as putative targets for Ras. PUBMED:8557659 EPMC:8557659


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000159

Ras proteins are signal-transducing GTPases that cycle between inactive GDP-bound and active GTP-bound forms. Ras is a prolific signalling molecule interacting with a spectrum of effector molecules and acting through more than one signalling pathway. A domain of about 100 residues, termed RA for RalGDS/AF-6 or Ras-Associating, interacts with Ras and other small GTPases. It occurs in one or two copies in a variety of signalling molecules. It can be found associated with many other domains, such as PDZ, Dilute (DIL), GEF, myosin motor, IQ, C1, C2, protein kinase, VPS9 or sterile alpha motif (SAM) [ PUBMED:8987396 , PUBMED:11723130 ].

Structurally, the RA domain of RalGDS consists of a five-stranded mixed beta-sheet interrupted by a 12 residue alpha-helix and two additional small alpha-helices. The structure of the RA domain belongs to the ubiquitin alpha/beta roll superfold and is similar to that of the RBD domain and the N-terminal third of the FERM domain [ PUBMED:9253406 , PUBMED:10334925 ]. The RA domain forms a homodimer where the interdimer surface is composed of two cysteines (Cys 2 in each monomer) forming an intermolecular disulfide bond and two interacting intermolecular antiparallel beta-sheets [ PUBMED:9253406 ]. The major interaction between Ras and RalGDS RA domain occurs between two antiparallel beta-strands: beta 2 of Ras and beta 2 of RA. This interaction occurs both at the backbone as well as the side chain level [ PUBMED:9628477 ].

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...

Loading domain graphics...

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
(39)
Full
(24686)
Representative proteomes UniProt
(38783)
RP15
(3063)
RP35
(7331)
RP55
(17997)
RP75
(25054)
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
(39)
Full
(24686)
Representative proteomes UniProt
(38783)
RP15
(3063)
RP35
(7331)
RP55
(17997)
RP75
(25054)
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
(39)
Full
(24686)
Representative proteomes UniProt
(38783)
RP15
(3063)
RP35
(7331)
RP55
(17997)
RP75
(25054)
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: Alignment kindly provided by SMART
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: SMART
Number in seed: 39
Number in full: 24686
Average length of the domain: 91.20 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 9.56 %

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 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 93
Family (HMM) version: 26
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

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

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 RA domain has been found. There are 49 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.

Loading structure mapping...

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
A0A0A1EI90 View 3D Structure Click here
A0A0G2JV91 View 3D Structure Click here
A0A0G2K6E6 View 3D Structure Click here
A0A0G2K7I9 View 3D Structure Click here
A0A0G2K961 View 3D Structure Click here
A0A0R4IFD5 View 3D Structure Click here
A0A0R4IIX0 View 3D Structure Click here
A0A140LH27 View 3D Structure Click here
A0A1D8PJE4 View 3D Structure Click here
A0A286YBW7 View 3D Structure Click here
A0A2R8PW91 View 3D Structure Click here
A0A2R8PZ15 View 3D Structure Click here
A0A2R8Q1P8 View 3D Structure Click here
A0A2R8Q8F0 View 3D Structure Click here
A0A2R8QGM1 View 3D Structure Click here
A0A2R8QKP7 View 3D Structure Click here
A0A2R8QUR4 View 3D Structure Click here
A0A2R8RIY0 View 3D Structure Click here
A0A2R8RWN2 View 3D Structure Click here
A0A2R8RZT1 View 3D Structure Click here
A7UA95 View 3D Structure Click here
A9C3N2 View 3D Structure Click here
B0BNA2 View 3D Structure Click here
B0S541 View 3D Structure Click here
B0S750 View 3D Structure Click here
B2RTY4 View 3D Structure Click here
B8JII7 View 3D Structure Click here
D3ZDZ1 View 3D Structure Click here
D3ZEY4 View 3D Structure Click here
D3ZTL8 View 3D Structure Click here
D4A1Z8 View 3D Structure Click here
D4A6C4 View 3D Structure Click here
D4AAU5 View 3D Structure Click here
D4ACL6 View 3D Structure Click here
D4ADX8 View 3D Structure Click here
E7EXR8 View 3D Structure Click here
E7EY43 View 3D Structure Click here
E7EZE7 View 3D Structure Click here
E7EZG2 View 3D Structure Click here
E7F3F0 View 3D Structure Click here