Summary: Replication factor C C-terminal domain
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Replication factor C C-terminal domain Provide feedback
This is the C-terminal domain of RFC (replication factor-C) protein of the clamp loader complex which binds to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA). The five modules of RFC assemble into a right-handed spiral, which results in only three of the five RFC subunits (RFC-A, RFC-B and RFC-C) making contact with PCNA, leaving a wedge-shaped gap between RFC-E and the PCNA clamp-loader complex. The C-terminal is vital for the correct orientation of RFC-E with respect to RFC-A [1].
Literature references
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Bowman GD, O'Donnell M, Kuriyan J; , Nature. 2004;429:724-730.: Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex. PUBMED:15201901 EPMC:15201901
Internal database links
SCOOP: | AAA_11 AAA_16 AAA_19 AAA_assoc_2 |
External database links
SCOP: | 1sxj |
This tab holds annotation information from the InterPro database.
InterPro entry IPR013748
This is the C-terminal domain of RFC (replication factor-C) protein of the clamp loader complex which binds to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA). The five modules of RFC assemble into a right-handed spiral, which results in only three of the five RFC subunits (RFC-A, RFC-B and RFC-C) making contact with PCNA, leaving a wedge-shaped gap between RFC-E and the PCNA clamp-loader complex. The C-terminal is vital for the correct orientation of RFC-E with respect to RFC-A [PUBMED:15201901].
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan post-AAA (CL0604), which has the following description:
According to SCOP this superfamily contains a 5 helical bundle domain that is found to the C-terminus of a P-loop AAA domain.
The clan contains the following 5 members:
DNA_pol3_delt_C DNA_pol3_gamma3 DNApol3-delta_C MgsA_C Rep_fac_CAlignments
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...
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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.
Seed (321) |
Full (4468) |
Representative proteomes | UniProt (8897) |
NCBI (9618) |
Meta (137) |
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RP15 (836) |
RP35 (2014) |
RP55 (3314) |
RP75 (4785) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (321) |
Full (4468) |
Representative proteomes | UniProt (8897) |
NCBI (9618) |
Meta (137) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (836) |
RP35 (2014) |
RP55 (3314) |
RP75 (4785) |
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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: | Pfam-B_930 (release 18.0) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Mistry J |
Number in seed: | 321 |
Number in full: | 4468 |
Average length of the domain: | 87.10 aa |
Average identity of full alignment: | 22 % |
Average coverage of the sequence by the domain: | 23.86 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 88 | ||||||||||||
Family (HMM) version: | 12 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There are 6 interactions for this family. More...
RFC1 Rep_fac_C AAA DNA_pol3_delta2 AAA DNA_pol3_delta2Structures
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 Rep_fac_C domain has been found. There are 18 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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