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26  structures 1458  species 0  interactions 2362  sequences 48  architectures

Family: RPC5 (PF04801)

Summary: RPC5 protein

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.

RPC5 protein Provide feedback

This family represents the RPC5 protein which is part of the RNA polymerase III complex [1-3].

Literature references

  1. Hoffmann NA, Jakobi AJ, Moreno-Morcillo M, Glatt S, Kosinski J, Hagen WJ, Sachse C, Muller CW;, Nature. 2015;528:231-236.: Molecular structures of unbound and transcribing RNA polymerase III. PUBMED:26605533 EPMC:26605533

  2. Han Y, Yan C, Fishbain S, Ivanov I, He Y;, Cell Discov. 2018;4:40.: Structural visualization of RNA polymerase III transcription machineries. PUBMED:30083386 EPMC:30083386

  3. Vorlander MK, Khatter H, Wetzel R, Hagen WJH, Muller CW;, Nature. 2018;553:295-300.: Molecular mechanism of promoter opening by RNA polymerase III. PUBMED:29345638 EPMC:29345638

This tab holds annotation information from the InterPro database.

InterPro entry IPR006886

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. RNA polymerase III (Pol III) is a complex consisting of 17 subunits, which synthesizes small RNAs, such as 5S rRNA and tRNAs. Pol III is essential for efficient transcription from both the type 2 VAI and type 3 U6 RNA polymerase III promoters and plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses, being involved in innate immune response, as it induces type I interferon and NF-Kappa-B through the RIG-I pathway [ PUBMED:19631370 ]. Subunit C5 is a specific peripheric component of RNA polymerase III complex. This subunit forms a subcomplex with RPC4 which is close to the active centre allowing the formation of the open promoter complex and facilitates termination and reinitiation. RPC5 mutations are associated with impaired type I INF and increased susceptibility to viral infections [ PUBMED:32843346 ].

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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Pfam Clan

This family is a member of clan Triple_barrel (CL0662), which has the following description:

Members of this superfamily adopt a triple barrel fold. This fold was first identified in the structure of the homodimer of RAP30 and RAP74. The two proteins form a single core structure composed of three interwoven beta barrels [1]. The central barrel is composed of beta strands from both heterodimer subunits. A similar fold has been observed in the heterodimer of TAF1 and TAF7 [2].

The clan contains the following 9 members:

DUF3591 RNA_pol_I_A49 RNA_pol_Rpc4 RNA_polI_A34 RNase_H2_suC RPC5 TAFII55_N TFIIF_beta_N Ydr279_N


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...

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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.

Representative proteomes UniProt
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

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Representative proteomes UniProt

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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.

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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...


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: Pfam-B_6302 (release 7.5)
Previous IDs: Sin_N;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A , Waterfield DI , Finn RD
Number in seed: 47
Number in full: 2362
Average length of the domain: 281.1 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 64.27 %

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 23.1 23.1
Trusted cut-off 23.4 23.1
Noise cut-off 22.7 22.9
Model length: 429
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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


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


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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 RPC5 domain has been found. There are 26 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