Summary: Ras association (RalGDS/AF-6) domain
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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
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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
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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
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Ponting CP, Benjamin DR; , Trends Biochem Sci 1996;21:422-425.: A novel family of Ras-binding domains. PUBMED:8987396 EPMC:8987396
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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
SCOOP: | FERM_N Ras_bdg_2 |
Similarity to PfamA using HHSearch: | RBD TUG-UBL1 Ras_bdg_2 |
External database links
HOMSTRAD: | RA |
SCOP: | 1lxd |
SMART: | RA |
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.
Biological process | signal transduction (GO:0007165) |
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 Ubiquitin (CL0072), which has the following description:
This family includes proteins that share the ubiquitin fold. It currently unites four SCOP superfamilies.
The clan contains the following 74 members:
APG12 APG5 Atg8 AUX_IAA B1 BILBO1_N Blt1 Caps_synth_GfcC CHIPS CIDE-N Cobl CRIM DCX DIX DUF2407 DUF348 DUF4430 DWNN FERM_f0 FERM_N FERM_N_2 Flg_new Formin_GBD_N GABP-alpha IgG_binding_B Kindlin_2_N Lambda_tail_I Mub_B2 MucBP MucBP_2 Multi_ubiq NLE NQRA_SLBB Oxidored_molyb Par3_HAL_N_term PB1 Phenol_monoox PI3K_p85B PI3K_rbd Prok_Ub RA Rad60-SLD Rad60-SLD_2 Ras_bdg_2 RAWUL RBD SAP18 Sde2_N_Ubi SHIRT SLBB Staphylokinase TBK1_ULD TGS ThiS ThiS-like TmoB TUG-UBL1 Tugs Ub-Mut7C Ub-RnfH ubiquitin Ubiquitin_2 Ubiquitin_3 Ubiquitin_4 Ubiquitin_5 UBX Ufm1 ULD UN_NPL4 Urm1 USP7_C2 USP7_ICP0_bdg YchF-GTPase_C YukDAlignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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 (40) |
Full (9270) |
Representative proteomes | UniProt (14370) |
NCBI (33884) |
Meta (3) |
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RP15 (1820) |
RP35 (3694) |
RP55 (6268) |
RP75 (7536) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
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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 (40) |
Full (9270) |
Representative proteomes | UniProt (14370) |
NCBI (33884) |
Meta (3) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (1820) |
RP35 (3694) |
RP55 (6268) |
RP75 (7536) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Alignment kindly provided by SMART |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: | SMART |
Number in seed: | 40 |
Number in full: | 9270 |
Average length of the domain: | 91.00 aa |
Average identity of full alignment: | 17 % |
Average coverage of the sequence by the domain: | 10.54 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 93 | ||||||||||||
Family (HMM) version: | 23 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 45 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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