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83  structures 1470  species 0  interactions 7630  sequences 221  architectures

Family: Ran_BP1 (PF00638)

Summary: RanBP1 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.

RanBP1 domain Provide feedback

No Pfam abstract.

Literature references

  1. Di Matteo G, Fuschi P, Zerfass K, Moretti S, Ricordy R, Cenciarelli C, Tripodi M, Jansen-Durr P, Lavia P; , Cell Growth Differ 1995;6:1213-1224.: Transcriptional control of the Htf9-A/RanBP-1 gene during the cell cycle. PUBMED:8845298 EPMC:8845298


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000156

Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran Binding Protein 1 (RanBP1) has guanine nucleotide dissociation inhibitory activity, specific for the GTP form of Ran and also functions to stimulate Ran GTPase activating protein(GAP)-mediated GTP hydrolysis by Ran. RanBP1 contributes to maintaining the gradient of RanGTP across the nuclear envelope high (GDI activity) or the cytoplasmic levels of RanGTP low (GAP cofactor) [ PUBMED:12019565 ].

All RanBP1 proteins contain an approx 150 amino acid residue Ran binding domain. Ran BP1 binds directly to RanGTP with high affinity. There are four sites of contact between Ran and the Ran binding domain. One of these involves binding of the C-terminal segment of Ran to a groove on the Ran binding domain that is analogous to the surface utilised in the EVH1-peptide interaction [ PUBMED:10404224 ]. Nup358 contains four Ran binding domains. The structure of the first of these is known [ PUBMED:10078529 ].

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...

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
(8)
Full
(7630)
Representative proteomes UniProt
(13421)
RP15
(1447)
RP35
(3446)
RP55
(6285)
RP75
(8409)
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
(8)
Full
(7630)
Representative proteomes UniProt
(13421)
RP15
(1447)
RP35
(3446)
RP55
(6285)
RP75
(8409)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(8)
Full
(7630)
Representative proteomes UniProt
(13421)
RP15
(1447)
RP35
(3446)
RP55
(6285)
RP75
(8409)
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: Prosite
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 8
Number in full: 7630
Average length of the domain: 115.90 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 21.89 %

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 23.2 23.2
Trusted cut-off 23.2 23.2
Noise cut-off 23.1 23.1
Model length: 122
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Selections

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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...

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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 Ran_BP1 domain has been found. There are 83 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
A0A096MJ81 View 3D Structure Click here
A0A1D6E286 View 3D Structure Click here
A0A1D6JZE5 View 3D Structure Click here
A0A1D6M2N3 View 3D Structure Click here
A0A1D6PCR6 View 3D Structure Click here
A0A1D8PHF9 View 3D Structure Click here
A0A1D8PNP6 View 3D Structure Click here
A0A1D8PRQ3 View 3D Structure Click here
A4HVS6 View 3D Structure Click here
A6NKT7 View 3D Structure Click here
A6NKT7 View 3D Structure Click here
B4FYD7 View 3D Structure Click here
B6T5R1 View 3D Structure Click here
D4A2G9 View 3D Structure Click here
F1Q591 View 3D Structure Click here
F1R0E4 View 3D Structure Click here
I1J7C7 View 3D Structure Click here
I1JA30 View 3D Structure Click here
I1LDC1 View 3D Structure Click here
I1LGI3 View 3D Structure Click here
I1M5M5 View 3D Structure Click here
I1MCM4 View 3D Structure Click here
I1NH59 View 3D Structure Click here
K7DY47 View 3D Structure Click here
K7KD30 View 3D Structure Click here
K7V4N5 View 3D Structure Click here
M0RD63 View 3D Structure Click here
O08587 View 3D Structure Click here
O14715 View 3D Structure Click here
O14715 View 3D Structure Click here
P0DJD0 View 3D Structure Click here
P0DJD0 View 3D Structure Click here
P0DJD1 View 3D Structure Click here
P0DJD1 View 3D Structure Click here
P32499 View 3D Structure Click here
P34022 View 3D Structure Click here
P40517 View 3D Structure Click here
P41920 View 3D Structure Click here
P43487 View 3D Structure Click here
P92985 View 3D Structure Click here
Q09146 View 3D Structure Click here
Q09717 View 3D Structure Click here
Q0DIY4 View 3D Structure Click here
Q10FH5 View 3D Structure Click here
Q10MW8 View 3D Structure Click here
Q21961 View 3D Structure Click here
Q3V2K7 View 3D Structure Click here
Q4DKB9 View 3D Structure Click here
Q4DSH6 View 3D Structure Click here
Q54KD9 View 3D Structure Click here
Q54YE9 View 3D Structure Click here
Q5W645 View 3D Structure Click here
Q6AYL1 View 3D Structure Click here
Q6NWK3 View 3D Structure Click here
Q6PCR4 View 3D Structure Click here
Q6PDH4 View 3D Structure Click here
Q76NN6 View 3D Structure Click here
Q7K0D8 View 3D Structure Click here
Q7Z3J3 View 3D Structure Click here
Q7Z3J3 View 3D Structure Click here
Q86G90 View 3D Structure Click here
Q86G90 View 3D Structure Click here
Q86G90 View 3D Structure Click here
Q86VV4 View 3D Structure Click here
Q8RWG8 View 3D Structure Click here
Q93ZH3 View 3D Structure Click here
Q99666 View 3D Structure Click here
Q99666 View 3D Structure Click here
Q9C829 View 3D Structure Click here
Q9CT10 View 3D Structure Click here
Q9H6Z4 View 3D Structure Click here
Q9JIH2 View 3D Structure Click here
Q9LMK7 View 3D Structure Click here
Q9LW88 View 3D Structure Click here
Q9UKX7 View 3D Structure Click here
Q9USL4 View 3D Structure Click here
Q9VCI7 View 3D Structure Click here