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48  structures 1157  species 0  interactions 18419  sequences 541  architectures

Family: RA (PF00788)

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

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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...

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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...

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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
(18419)
Representative proteomes UniProt
(32051)
RP15
(2486)
RP35
(6464)
RP55
(15790)
RP75
(21837)
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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.

Format an alignment

  Seed
(39)
Full
(18419)
Representative proteomes UniProt
(32051)
RP15
(2486)
RP35
(6464)
RP55
(15790)
RP75
(21837)
Alignment:
Format:
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Sequence:
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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
(18419)
Representative proteomes UniProt
(32051)
RP15
(2486)
RP35
(6464)
RP55
(15790)
RP75
(21837)
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: 18419
Average length of the domain: 90.80 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 9.86 %

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 20.6 20.6
Trusted cut-off 20.6 20.6
Noise cut-off 20.5 20.5
Model length: 93
Family (HMM) version: 25
Download: download the raw HMM for this family

Species distribution

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Selections

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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 RA domain has been found. There are 48 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
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
E7F4R0 View 3D Structure Click here
E7F4R0 View 3D Structure Click here
E7F662 View 3D Structure Click here
E7F7Y0 View 3D Structure Click here
E7FC22 View 3D Structure Click here
E7FFI5 View 3D Structure Click here
E7FFP7 View 3D Structure Click here
E9QDK1 View 3D Structure Click here
E9QI83 View 3D Structure Click here
F0IWT2 View 3D Structure Click here
F1LM60 View 3D Structure Click here
F1M386 View 3D Structure Click here
F1M6I2 View 3D Structure Click here
F1Q4V7 View 3D Structure Click here
F1QJA9 View 3D Structure Click here
F1QSC3 View 3D Structure Click here
F1QX11 View 3D Structure Click here
F1QZE7 View 3D Structure Click here
F1RDI1 View 3D Structure Click here
F1RET1 View 3D Structure Click here
F2Z3U3 View 3D Structure Click here
G5EDB9 View 3D Structure Click here
G5EFI8 View 3D Structure Click here
G5EFI8 View 3D Structure Click here
I3IT01 View 3D Structure Click here
I3ITQ9 View 3D Structure Click here
O15211 View 3D Structure Click here
O35141 View 3D Structure Click here
O35889 View 3D Structure Click here
O35889 View 3D Structure Click here
O88900 View 3D Structure Click here
P0CE43 View 3D Structure Click here
P25344 View 3D Structure Click here
P36622 View 3D Structure Click here
P50749 View 3D Structure Click here
P52824 View 3D Structure Click here
P55196 View 3D Structure Click here
P55196 View 3D Structure Click here
P91575 View 3D Structure Click here
P91575 View 3D Structure Click here
Q02833 View 3D Structure Click here
Q03160 View 3D Structure Click here
Q03385 View 3D Structure Click here
Q03386 View 3D Structure Click here
Q0VG64 View 3D Structure Click here
Q12967 View 3D Structure Click here
Q13322 View 3D Structure Click here
Q13459 View 3D Structure Click here
Q13671 View 3D Structure Click here
Q14449 View 3D Structure Click here
Q14451 View 3D Structure Click here
Q17860 View 3D Structure Click here
Q17860 View 3D Structure Click here
Q19852 View 3D Structure Click here
Q1L8B0 View 3D Structure Click here
Q1ZXE2 View 3D Structure Click here
Q22744 View 3D Structure Click here
Q3B7D5 View 3D Structure Click here
Q3B7L1 View 3D Structure Click here
Q3MIN7 View 3D Structure Click here
Q3U0S6 View 3D Structure Click here
Q3UHD6 View 3D Structure Click here
Q3UYI5 View 3D Structure Click here
Q3V0P3 View 3D Structure Click here
Q4LDD4 View 3D Structure Click here
Q4QR82 View 3D Structure Click here
Q54Q33 View 3D Structure Click here
Q54Q60 View 3D Structure Click here
Q54VR6 View 3D Structure Click here
Q566C5 View 3D Structure Click here
Q5EBH1 View 3D Structure Click here
Q5FAQ9 View 3D Structure Click here
Q5NCJ1 View 3D Structure Click here
Q5TZF0 View 3D Structure Click here
Q5U651 View 3D Structure Click here
Q60695 View 3D Structure Click here
Q60760 View 3D Structure Click here
Q61193 View 3D Structure Click here
Q63358 View 3D Structure Click here
Q66HV2 View 3D Structure Click here
Q68EG5 View 3D Structure Click here
Q69Z89 View 3D Structure Click here
Q6IFT4 View 3D Structure Click here
Q6MGC5 View 3D Structure Click here
Q6P112 View 3D Structure Click here
Q6P3G2 View 3D Structure Click here
Q6P5E8 View 3D Structure Click here
Q6PFT9 View 3D Structure Click here
Q6REY9 View 3D Structure Click here
Q6ZTQ3 View 3D Structure Click here
Q70E73 View 3D Structure Click here
Q7Z5R6 View 3D Structure Click here
Q7Z736 View 3D Structure Click here
Q80UQ2 View 3D Structure Click here
Q86NJ4 View 3D Structure Click here
Q86NJ4 View 3D Structure Click here
Q86WH2 View 3D Structure Click here
Q8BMS9 View 3D Structure Click here
Q8BZ05 View 3D Structure Click here
Q8C170 View 3D Structure Click here
Q8CB96 View 3D Structure Click here
Q8CHG7 View 3D Structure Click here
Q8CJ96 View 3D Structure Click here
Q8K4S1 View 3D Structure Click here
Q8K4V4 View 3D Structure Click here
Q8MQW8 View 3D Structure Click here
Q8NHQ8 View 3D Structure Click here
Q8R5A3 View 3D Structure Click here
Q8R5G7 View 3D Structure Click here
Q8TEU7 View 3D Structure Click here
Q8VCE9 View 3D Structure Click here
Q8WWN8 View 3D Structure Click here
Q8WWW0 View 3D Structure Click here
Q8WYP3 View 3D Structure Click here
Q8WZ64 View 3D Structure Click here
Q96JH8 View 3D Structure Click here
Q96L92 View 3D Structure Click here
Q96P48 View 3D Structure Click here
Q99MK9 View 3D Structure Click here
Q99P51 View 3D Structure Click here
Q99P84 View 3D Structure Click here
Q9D684 View 3D Structure Click here
Q9DD19 View 3D Structure Click here
Q9H2L5 View 3D Structure Click here
Q9HD67 View 3D Structure Click here
Q9JLM9 View 3D Structure Click here
Q9NS23 View 3D Structure Click here
Q9NZL6 View 3D Structure Click here
Q9P212 View 3D Structure Click here
Q9P2F6 View 3D Structure Click here
Q9QY06 View 3D Structure Click here
Q9QZC5 View 3D Structure Click here
Q9QZQ1 View 3D Structure Click here
Q9QZQ1 View 3D Structure Click here
Q9VBP2 View 3D Structure Click here
Q9VCQ7 View 3D Structure Click here
Q9VMF3 View 3D Structure Click here
Q9VML8 View 3D Structure Click here
Q9VML8 View 3D Structure Click here
Q9VN82 View 3D Structure Click here
Q9VN82 View 3D Structure Click here
Q9VWB7 View 3D Structure Click here
Q9W486 View 3D Structure Click here
Q9Y4G8 View 3D Structure Click here
Q9Z1N3 View 3D Structure Click here
R4GER0 View 3D Structure Click here
X1WHA5 View 3D Structure Click here
X4YX01 View 3D Structure Click here