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90  structures 1201  species 0  interactions 13029  sequences 326  architectures

Family: RasGEF_N (PF00618)

Summary: RasGEF N-terminal motif

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RasGEF N-terminal motif Provide feedback

A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this motif/domain N-terminal to the RasGef (Cdc25-like) domain.

Literature references

  1. Boguski MS, McCormick F; , Nature 1993;366:643-654.: Proteins regulating Ras and its relatives. PUBMED:8259209 EPMC:8259209

  2. Quilliam LA, Khosravi-Far R, Huff SY, Der CJ; , Bioessays 1995;17:395-404.: Guanine nucleotide exchange factors: activators of the Ras superfamily of proteins. PUBMED:7786285 EPMC:7786285

  3. Li N, Batzer A, Daly R, Yajnik V, Skolnik E, Chardin P, Bar-Sagi D, Margolis B, Schlessinger J; , Nature 1993;363:85-88.: Guanine-nucleotide-releasing factor hSos1 binds to Grb2 and links receptor tyrosine kinases to Ras signalling. PUBMED:8479541 EPMC:8479541

  4. Skolnik EY, Batzer A, Li N, Lee CH, Lowenstein E, Mohammadi M, Margolis B, Schlessinger J; , Science 1993;260:1953-1955.: The function of GRB2 in linking the insulin receptor to Ras signaling pathways. PUBMED:8316835 EPMC:8316835


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000651

The crystal structure of the GEF region of human Sos1 complexes with Ras has been solved [ PUBMED:9690470 ]. The structure consists of two distinct alpha helical structural domains: the N-terminal domain which seems to have a purely structural role and the C-terminal domain which is sufficient for catalytic activity and contains all residues that interact with Ras. A main feature of the catalytic domain is the protrusion of a helical hairpin important for the nucleotide-exchange mechanism. The N-terminal domain is likely to be important for the stability and correct placement of the hairpin structure.

This entry represents a domain found in several GEF for Ras-like small GTPases which lies N-terminal to the RasGef (Cdc25-like) domain.

The N-terminal domain of guanine nucleotide exchange factor (GEF) for Ras-like GTPases is also called REM domain (Ras exchanger motif). REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few [ PUBMED:18541156 , PUBMED:18236214 , PUBMED:7786285 , PUBMED:8259209 , PUBMED:8479541 , PUBMED:16452984 , PUBMED:12628188 , PUBMED:9690470 ].

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 RAS_GEF_N (CL0542), which has the following description:

This is the more N-terminal domain of the RAS-GEF superfamily.

The clan contains the following 2 members:

RasGEF_N RasGEF_N_2

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
(52)
Full
(13029)
Representative proteomes UniProt
(21548)
RP15
(1836)
RP35
(4712)
RP55
(10592)
RP75
(14631)
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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
(52)
Full
(13029)
Representative proteomes UniProt
(21548)
RP15
(1836)
RP35
(4712)
RP55
(10592)
RP75
(14631)
Alignment:
Format:
Order:
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
(52)
Full
(13029)
Representative proteomes UniProt
(21548)
RP15
(1836)
RP35
(4712)
RP55
(10592)
RP75
(14631)
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: SMART
Previous IDs: RasGEFN;
Type: Domain
Sequence Ontology: SO:0000417
Author: Ponting CP , Schultz J, Bork P
Number in seed: 52
Number in full: 13029
Average length of the domain: 106.50 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 9.88 %

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 28.3 28.3
Trusted cut-off 28.3 28.3
Noise cut-off 28.2 28.2
Model length: 105
Family (HMM) version: 22
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 RasGEF_N domain has been found. There are 90 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
A0A0G2JE67 View 3D Structure Click here
A0A0G2JGB2 View 3D Structure Click here
A0A0G2JGX9 View 3D Structure Click here
A0A0G2JV91 View 3D Structure Click here
A0A0G2JW65 View 3D Structure Click here
A0A0G2K922 View 3D Structure Click here
A0A0G2K961 View 3D Structure Click here
A0A0N4SVR5 View 3D Structure Click here
A0A0R4IM06 View 3D Structure Click here
A0A1D8PHR4 View 3D Structure Click here
A0A1D8PTC8 View 3D Structure Click here
A0A2R8PZ15 View 3D Structure Click here
A0A2R8Q8F0 View 3D Structure Click here
A0A2R8QGM1 View 3D Structure Click here
A0A2R8QKP7 View 3D Structure Click here
A0A2R8QV10 View 3D Structure Click here
A0A2R8RZT1 View 3D Structure Click here
A1Z6P8 View 3D Structure Click here
A2CEA7 View 3D Structure Click here
B0M0P8 View 3D Structure Click here
B0S750 View 3D Structure Click here
B2RW27 View 3D Structure Click here
D3Z0W7 View 3D Structure Click here
D3Z810 View 3D Structure Click here
D3ZE80 View 3D Structure Click here
D3ZHB9 View 3D Structure Click here
D3ZJN7 View 3D Structure Click here
D3ZJX4 View 3D Structure Click here
D3ZKT3 View 3D Structure Click here
D3ZLG9 View 3D Structure Click here
D3ZPF4 View 3D Structure Click here
D3ZTL8 View 3D Structure Click here
D3ZVN9 View 3D Structure Click here
D3ZWL3 View 3D Structure Click here
D3ZYU2 View 3D Structure Click here
D3ZZV7 View 3D Structure Click here
D4A3T0 View 3D Structure Click here
D4A8Q2 View 3D Structure Click here
D4ADU5 View 3D Structure Click here
E7F4B2 View 3D Structure Click here
E7F7V2 View 3D Structure Click here
E7FBN7 View 3D Structure Click here
E7FDC9 View 3D Structure Click here
E7FFI6 View 3D Structure Click here
E9QDY7 View 3D Structure Click here
E9QI83 View 3D Structure Click here
F1M386 View 3D Structure Click here
F1M8L9 View 3D Structure Click here
F1MAI3 View 3D Structure Click here
F1QZX0 View 3D Structure Click here
F1R019 View 3D Structure Click here
F1RDI1 View 3D Structure Click here
G5EDB9 View 3D Structure Click here
H2KZX7 View 3D Structure Click here
I3IT01 View 3D Structure Click here
J3QMS8 View 3D Structure Click here
J3QNG1 View 3D Structure Click here
K7N5P2 View 3D Structure Click here
L7N481 View 3D Structure Click here
M0R4F2 View 3D Structure Click here
O14827 View 3D Structure Click here
O15211 View 3D Structure Click here
O77086 View 3D Structure Click here
O95267 View 3D Structure Click here
O95398 View 3D Structure Click here
P04821 View 3D Structure Click here
P07866 View 3D Structure Click here
P0C643 View 3D Structure Click here
P26674 View 3D Structure Click here
P26675 View 3D Structure Click here
P27671 View 3D Structure Click here
P28818 View 3D Structure Click here
P34578 View 3D Structure Click here
P39960 View 3D Structure Click here
P43069 View 3D Structure Click here
P70392 View 3D Structure Click here
P83900 View 3D Structure Click here
Q02384 View 3D Structure Click here
Q03385 View 3D Structure Click here
Q03386 View 3D Structure Click here
Q07889 View 3D Structure Click here
Q07890 View 3D Structure Click here
Q0KK55 View 3D Structure Click here
Q0VAM2 View 3D Structure Click here
Q12967 View 3D Structure Click here
Q13905 View 3D Structure Click here
Q13972 View 3D Structure Click here
Q19852 View 3D Structure Click here
Q3MIN7 View 3D Structure Click here
Q3UHC1 View 3D Structure Click here
Q3UYI5 View 3D Structure Click here
Q3V0H9 View 3D Structure Click here
Q4DCC1 View 3D Structure Click here
Q4DG49 View 3D Structure Click here
Q4E1N0 View 3D Structure Click here
Q54C94 View 3D Structure Click here
Q54FF3 View 3D Structure Click here
Q54H95 View 3D Structure Click here
Q54PQ4 View 3D Structure Click here
Q54S40 View 3D Structure Click here
Q54TK8 View 3D Structure Click here
Q552M5 View 3D Structure Click here
Q55EC7 View 3D Structure Click here
Q55FD8 View 3D Structure Click here
Q55GH9 View 3D Structure Click here
Q5AGW7 View 3D Structure Click here
Q5NCJ1 View 3D Structure Click here
Q60695 View 3D Structure Click here
Q61193 View 3D Structure Click here
Q62245 View 3D Structure Click here
Q6DBW1 View 3D Structure Click here
Q6DHR3 View 3D Structure Click here
Q6MGC5 View 3D Structure Click here
Q6P112 View 3D Structure Click here
Q76NI1 View 3D Structure Click here
Q7KTU3 View 3D Structure Click here
Q7LDG7 View 3D Structure Click here
Q80ZR8 View 3D Structure Click here
Q86G47 View 3D Structure Click here
Q8BVR5 View 3D Structure Click here
Q8C0Q9 View 3D Structure Click here
Q8CHG7 View 3D Structure Click here
Q8IS11 View 3D Structure Click here
Q8IS14 View 3D Structure Click here
Q8IS15 View 3D Structure Click here
Q8IS16 View 3D Structure Click here
Q8IS18 View 3D Structure Click here
Q8IS19 View 3D Structure Click here
Q8IS20 View 3D Structure Click here
Q8IS21 View 3D Structure Click here
Q8JZL7 View 3D Structure Click here
Q8MVR1 View 3D Structure Click here
Q8N431 View 3D Structure Click here
Q8N9B8 View 3D Structure Click here
Q8SSQ0 View 3D Structure Click here
Q8SSQ3 View 3D Structure Click here
Q8SSW7 View 3D Structure Click here
Q8ST25 View 3D Structure Click here
Q8TEU7 View 3D Structure Click here
Q8VCC8 View 3D Structure Click here
Q8WZA2 View 3D Structure Click here
Q92565 View 3D Structure Click here
Q99JE4 View 3D Structure Click here
Q9D300 View 3D Structure Click here
Q9D420 View 3D Structure Click here
Q9D506 View 3D Structure Click here
Q9D5E3 View 3D Structure Click here
Q9D991 View 3D Structure Click here
Q9EQZ6 View 3D Structure Click here
Q9N5D3 View 3D Structure Click here
Q9NZL6 View 3D Structure Click here
Q9QUG9 View 3D Structure Click here
Q9R1K8 View 3D Structure Click here
Q9USU1 View 3D Structure Click here
Q9VMF3 View 3D Structure Click here
Q9Y4G8 View 3D Structure Click here
Q9Z1C8 View 3D Structure Click here
Q9Z1S3 View 3D Structure Click here
W6RS10 View 3D Structure Click here