Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
414  structures 2284  species 0  interactions 111186  sequences 2234  architectures

Family: RCC1 (PF00415)

Summary: Regulator of chromosome condensation (RCC1) repeat

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

Regulator of chromosome condensation (RCC1) repeat Provide feedback

No Pfam abstract.

Literature references

  1. Renault L, Nassar N, Vetter I, Becker J, Klebe C, Roth M, Wittinghofer A; , Nature 1998;392:97-101.: The 1.7 A crystal structure of the regulator of chromosome condensation (RCC1) reveals a seven-bladed propeller. PUBMED:9510255 EPMC:9510255


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000408

The regulator of chromosome condensation (RCC1) [ PUBMED:8480369 ] is a eukaryotic protein which binds to chromatin and interacts with ran, a nuclear GTP-binding protein INTERPRO , to promote the loss of bound GDP and the uptake of fresh GTP, thus acting as a guanine-nucleotide dissociation stimulator (GDS). The interaction of RCC1 with ran probably plays an important role in the regulation of gene expression.

RCC1, known as PRP20 or SRM1 in yeast, pim1 in fission yeast and BJ1 in Drosophila, is a protein that contains seven tandem repeats of a domain of about 50 to 60 amino acids. As shown in the following schematic representation, the repeats make up the major part of the length of the protein. Outside the repeat region, there is just a small N-terminal domain of about 40 to 50 residues and, in the Drosophila protein only, a C-terminal domain of about 130 residues.

+----+-------+-------+-------+-------+-------+-------+-------+-------------+
|N-t.|Rpt. 1 |Rpt. 2 |Rpt. 3 |Rpt. 4 |Rpt. 5 |Rpt. 6 |Rpt. 7 | C-terminal  |
+----+-------+-------+-------+-------+-------+-------+-------+-------------+
The RCC1-type of repeat is also found in the X-linked retinitis pigmentosa GTPase regulator [ PUBMED:8817343 ]. The RCC repeats form a beta-propeller structure.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Pfam Clan

This family is a member of clan Beta_propeller (CL0186), which has the following description:

This large clan contains proteins that contain beta propellers. These are composed of between 6 and 8 repeats. The individual repeats are composed of a four stranded sheet. The clan includes families such as WD40 Pfam:PF00400 where the individual repeats are modeled. The clan also includes families where the entire propeller is modeled such as Pfam:PF02239 usually because the individual repeats are not discernible. These proteins carry out a very wide diversity of functions including catalysis.

The clan contains the following 112 members:

ANAPC1 ANAPC4_WD40 Arylesterase Arylsulfotran_2 Arylsulfotrans B_lectin BBS2_Mid BBS2_N Beta_propel Coatomer_WDAD CPSF_A CyRPA Cytochrom_D1 DCAF17 Dpp_8_9_N DPPIV_N DPPIV_rep DUF1513 DUF1668 DUF2415 DUF346 DUF3466 DUF3616 DUF3748 DUF4221 DUF4374 DUF4394 DUF4623 DUF4784 DUF4915 DUF4933 DUF4934 DUF5046 DUF5050 DUF5122 DUF5128 DUF5711 DUF839 eIF2A FG-GAP FG-GAP_2 FG-GAP_3 Frtz Ge1_WD40 Glu_cyclase_2 Glyoxal_oxid_N Gmad1 GSDH Helveticin_J HPS3_N HPS6 Hyd_WA IKI3 Itfg2 Kelch_1 Kelch_2 Kelch_3 Kelch_4 Kelch_5 Kelch_6 Lactonase Ldl_recept_b LGFP Lgl_C LVIVD Me-amine-dh_H MgpC MRJP Nbas_N NBCH_WD40 Neisseria_PilC NHL nos_propeller nos_propeller_2 Nucleoporin_N Nup160 Nup88 P1_N PALB2_WD40 PD40 Pectate_lyase22 Peptidase_S9_N PHTB1_N Phytase-like PQQ PQQ_2 PQQ_3 RAB3GAP2_N RAG2 RCC1 RCC1_2 Reg_prop RPE65 SBBP SBP56 SdiA-regulated Sema SGL SSL_N Str_synth TcdB_toxin_midN Tectonin TolB_like VID27 Vps16_N WD40 WD40_2 WD40_3 WD40_4 WD40_like WDCP YmzC

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
(101)
Full
(111186)
Representative proteomes UniProt
(192933)
RP15
(19934)
RP35
(46295)
RP55
(88472)
RP75
(120842)
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
(101)
Full
(111186)
Representative proteomes UniProt
(192933)
RP15
(19934)
RP35
(46295)
RP55
(88472)
RP75
(120842)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(101)
Full
(111186)
Representative proteomes UniProt
(192933)
RP15
(19934)
RP35
(46295)
RP55
(88472)
RP75
(120842)
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: Repeat
Sequence Ontology: SO:0001068
Author: Finn RD
Number in seed: 101
Number in full: 111186
Average length of the domain: 51.50 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 20.54 %

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 21.7 21.7
Trusted cut-off 21.7 21.7
Noise cut-off 21.6 21.6
Model length: 50
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 RCC1 domain has been found. There are 414 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.

Loading structure mapping...

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
A0A061AD48 View 3D Structure Click here
A0A0G2K8N9 View 3D Structure Click here
A0A0N7KL66 View 3D Structure Click here
A0A0P0V8V0 View 3D Structure Click here
A0A0P0VA80 View 3D Structure Click here
A0A0P0VD31 View 3D Structure Click here
A0A0P0VD89 View 3D Structure Click here
A0A0P0W020 View 3D Structure Click here
A0A0P0WDY2 View 3D Structure Click here
A0A0P0WH96 View 3D Structure Click here
A0A0P0WN65 View 3D Structure Click here
A0A0P0XLV2 View 3D Structure Click here
A0A0P0XQB6 View 3D Structure Click here
A0A0R0F9B9 View 3D Structure Click here
A0A0R0FRM1 View 3D Structure Click here
A0A0R0GIK8 View 3D Structure Click here
A0A0R0H8T6 View 3D Structure Click here
A0A0R0HMB0 View 3D Structure Click here
A0A0R0HRH0 View 3D Structure Click here
A0A0R0HUI7 View 3D Structure Click here
A0A0R0IEG5 View 3D Structure Click here
A0A0R0IUD7 View 3D Structure Click here
A0A0R0J3T6 View 3D Structure Click here
A0A0R0J9S6 View 3D Structure Click here
A0A0R0JML6 View 3D Structure Click here
A0A0R0JVE0 View 3D Structure Click here
A0A0R0K5W4 View 3D Structure Click here
A0A0R0KPM3 View 3D Structure Click here
A0A0R0L1B2 View 3D Structure Click here
A0A0R0L657 View 3D Structure Click here
A0A0R0L6A0 View 3D Structure Click here
A0A0R4IJG8 View 3D Structure Click here
A0A1D6E1T8 View 3D Structure Click here
A0A1D6E4Z3 View 3D Structure Click here
A0A1D6EMA5 View 3D Structure Click here
A0A1D6F0H9 View 3D Structure Click here
A0A1D6G2V2 View 3D Structure Click here
A0A1D6G3Z7 View 3D Structure Click here
A0A1D6G474 View 3D Structure Click here
A0A1D6G8I0 View 3D Structure Click here