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14  structures 54  species 0  interactions 102  sequences 11  architectures

Family: RanGAP1_C (PF07834)

Summary: RanGAP1 C-terminal domain

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RanGAP1 C-terminal domain Provide feedback

Ran-GTPase activating protein 1 (RanGAP1, P46061) is a GTPase activator for the nuclear Ras-related regulatory protein Ran, converting it to the putatively inactive GDP-bound state. Its C-terminal domain is required for RanGAP1 localisation at the vertebrate nuclear pore complex, and is sumoylated by the small ubiquitin-related modifier protein (SUMO-1, Q93068). This domain is composed almost entirely of helical substructures that are organised into an alpha-alpha superhelix fold, with the exception of the peptide containing the lysine residue required for SUMO-1 conjugation [1].

Literature references

  1. Bernier-Villamor V, Sampson DA, Matunis MJ, Lima CD; , Cell 2002;108:345-356.: Structural basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin-conjugating enzyme Ubc9 and RanGAP1. PUBMED:11853669 EPMC:11853669


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR009109

Ran GTPase is a ubiquitous protein required for nuclear transport, spindle assembly, nuclear assembly and mitotic cell cycle regulation. RanGTPase activating protein 1 (RanGAP1) is one of several RanGTPase accessory proteins. During interphase, RanGAP1 is located in the cytoplasm, while during mitosis it becomes associated with the kinetochores [PUBMED:12852855]. Cytoplasmic RanGAP1 is required for RanGTPase-directed nuclear transport. The activity of RanGAP1 requires the accessory protein RanBP1. RanBP1 facilitates RanGAP1 hydrolysis of Ran-GTP, both directly and by promoting the dissociation of Ran-GTP from transport receptors, which would otherwise block RanGAP1-mediated hydrolysis. RanGAP1 is thought to bind to the Switch 1 and Switch 2 regions of RanGTPase. The Switch 2 region can be buried in complexes with karyopherin-beta2, and requires the interaction with RanBP1 to permit RanGAP1 function. RanGAP1 can undergo SUMO (small ubiquitin-like modifier) modification, which targets RanGAP1 to RanBP2/Nup358 in the nuclear pore complex, and is required for association with the nuclear pore complex and for nuclear transport [PUBMED:11853669]. The enzymes involved in SUMO modification are located on the filaments of the nuclear pore complex.

The RanGAP1 N-terminal domain is fairly well conserved between vertebrate and fungal proteins, but yeast does not contain the C-terminal domain. The C-terminal domain is SUMO-modified and required for the localisation of RanGAP1 at the nuclear pore complex. The structure of the C-terminal domain is multihelical, consisting of two curved alpha/alpha layers in a right-handed superhelix.

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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.

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(3)
Full
(102)
Representative proteomes NCBI
(98)
Meta
(0)
RP15
(10)
RP35
(13)
RP55
(26)
RP75
(43)
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  Seed
(3)
Full
(102)
Representative proteomes NCBI
(98)
Meta
(0)
RP15
(10)
RP35
(13)
RP55
(26)
RP75
(43)
Alignment:
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Sequence:
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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
(3)
Full
(102)
Representative proteomes NCBI
(98)
Meta
(0)
RP15
(10)
RP35
(13)
RP55
(26)
RP75
(43)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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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.

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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_23411 (release 14.0)
Previous IDs: none
Type: Domain
Author: Fenech M
Number in seed: 3
Number in full: 102
Average length of the domain: 173.50 aa
Average identity of full alignment: 54 %
Average coverage of the sequence by the domain: 32.44 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 27.1 26.4
Noise cut-off 24.2 24.0
Model length: 183
Family (HMM) version: 6
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 RanGAP1_C domain has been found. There are 14 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 seqence.

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