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39  structures 1439  species 0  interactions 23716  sequences 554  architectures

Family: zf-RanBP (PF00641)

Summary: Zn-finger in Ran binding protein and others

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Zn-finger in Ran binding protein and others Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001876

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [ PUBMED:10529348 , PUBMED:15963892 , PUBMED:15718139 , PUBMED:17210253 , PUBMED:12665246 ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few [ PUBMED:11179890 ]. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.

This entry represents the zinc finger domain found in RanBP2 proteins. 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 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import [ PUBMED:12019565 ]. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP [ PUBMED:10318915 ].

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
(24)
Full
(23716)
Representative proteomes UniProt
(39214)
RP15
(3434)
RP35
(9439)
RP55
(17949)
RP75
(24536)
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
(24)
Full
(23716)
Representative proteomes UniProt
(39214)
RP15
(3434)
RP35
(9439)
RP55
(17949)
RP75
(24536)
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
(24)
Full
(23716)
Representative proteomes UniProt
(39214)
RP15
(3434)
RP35
(9439)
RP55
(17949)
RP75
(24536)
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: 24
Number in full: 23716
Average length of the domain: 29.80 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 7.96 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 17.0
Trusted cut-off 27.0 17.0
Noise cut-off 26.9 16.9
Model length: 30
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Viroids Viroids Unclassified sequence Unclassified sequence

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 zf-RanBP domain has been found. There are 39 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
A0A0B4J1A5 View 3D Structure Click here
A0A0G2JVC1 View 3D Structure Click here
A0A0G2JWR5 View 3D Structure Click here
A0A0G2KAS0 View 3D Structure Click here
A0A0G2KUM0 View 3D Structure Click here
A0A0R0ETV2 View 3D Structure Click here
A0A0R0EUK5 View 3D Structure Click here
A0A0R0HI47 View 3D Structure Click here
A0A0R0HRU5 View 3D Structure Click here
A0A0R0ICS0 View 3D Structure Click here
A0A0R0JPD4 View 3D Structure Click here
A0A0R0KFC2 View 3D Structure Click here
A0A0R0L0D4 View 3D Structure Click here
A0A0R0L9J3 View 3D Structure Click here
A0A0R4IVZ0 View 3D Structure Click here
A0A140UHY3 View 3D Structure Click here
A0A1D6EFV6 View 3D Structure Click here
A0A1D6EKM9 View 3D Structure Click here
A0A1D6EUN3 View 3D Structure Click here
A0A1D6IAU9 View 3D Structure Click here
A0A1D6IXA6 View 3D Structure Click here
A0A1D6J2I9 View 3D Structure Click here
A0A1D6KJ69 View 3D Structure Click here
A0A1D6MKY7 View 3D Structure Click here
A0A1D6NVS7 View 3D Structure Click here
A0A1D6PXP7 View 3D Structure Click here
A0A2R8Q9Z9 View 3D Structure Click here
A0A2R8RKD0 View 3D Structure Click here
A0A2R8RLN8 View 3D Structure Click here
A0JMQ9 View 3D Structure Click here
A1A5X7 View 3D Structure Click here
A4HUN2 View 3D Structure Click here
A4HXJ2 View 3D Structure Click here
A4HXT6 View 3D Structure Click here
A4ICJ4 View 3D Structure Click here
A4IGK4 View 3D Structure Click here
A6QP16 View 3D Structure Click here
A9JTG5 View 3D Structure Click here
B1H2Q2 View 3D Structure Click here
B2GV05 View 3D Structure Click here