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
-
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
SCOOP: | RCC1_2 |
Similarity to PfamA using HHSearch: | RCC1_2 RCC1_2 |
External database links
PROSITE: | PDOC00544 |
SCOP: | 1a12 |
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 80 members:
ANAPC4_WD40 Arylesterase Arylsulfotran_2 Arylsulfotrans BBS2_Mid Beta_propel Coatomer_WDAD CPSF_A CyRPA Cytochrom_D1 DPPIV_N DUF1513 DUF1668 DUF2415 DUF4221 DUF4933 DUF4934 DUF5046 DUF5050 DUF5122 DUF5128 DUF5711 DUF839 eIF2A FG-GAP FG-GAP_2 Frtz Ge1_WD40 Glu_cyclase_2 Gmad1 GSDH 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 MRJP Nbas_N Neisseria_PilC NHL Nucleoporin_N Nup160 PALB2_WD40 PD40 Pectate_lyase22 Peptidase_S9_N PHTB1_N Phytase-like PQQ PQQ_2 PQQ_3 RAG2 RCC1 RCC1_2 Reg_prop SBBP SBP56 SdiA-regulated SGL Str_synth TcdB_toxin_midN Tectonin TolB_like VCBS VID27 WD40 WD40_2 WD40_3 WD40_4 WD40_likeAlignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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 (65112) |
Representative proteomes | UniProt (118087) |
NCBI (238061) |
Meta (3246) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (10897) |
RP35 (28853) |
RP55 (49453) |
RP75 (70462) |
||||||
Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
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 (65112) |
Representative proteomes | UniProt (118087) |
NCBI (238061) |
Meta (3246) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (10897) |
RP35 (28853) |
RP55 (49453) |
RP75 (70462) |
||||||
Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Prosite |
Previous IDs: | none |
Type: | Repeat |
Sequence Ontology: | SO:0001068 |
Author: |
Finn RD |
Number in seed: | 101 |
Number in full: | 65112 |
Average length of the domain: | 51.60 aa |
Average identity of full alignment: | 30 % |
Average coverage of the sequence by the domain: | 21.00 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
|
||||||||||||
Model details: |
|
||||||||||||
Model length: | 50 | ||||||||||||
Family (HMM) version: | 19 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
Sunburst controls
HideWeight segments by...
Change the size of the sunburst
Colour assignments
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
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...
Tree controls
HideThe 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 337 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...