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160  structures 1652  species 0  interactions 3406  sequences 53  architectures

Family: RNA_pol_Rpb4 (PF03874)

Summary: RNA polymerase Rpb4

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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.

RNA polymerase Rpb4 Provide feedback

This family includes the Rpb4 protein. This family also includes C17 (aka CGRP-RCP) is an essential subunit of RNA polymerase III. C17 forms a subcomplex with C25 [5] which is likely to be the counterpart of subcomplex Rpb4/7 in Pol II [4].

Literature references

  1. Todone F, Brick P, Werner F, Weinzierl RO, Onesti S; , Mol Cell 2001;8:1137-1143.: Structure of an archaeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex. PUBMED:11741548 EPMC:11741548

  2. Siaut M, Zaros C, Levivier E, Ferri ML, Court M, Werner M, Callebaut I, Thuriaux P, Sentenac A, Conesa C; , Mol Cell Biol. 2003;23:195-205.: An Rpb4/Rpb7-like complex in yeast RNA polymerase III contains the orthologue of mammalian CGRP-RCP. PUBMED:12482973 EPMC:12482973

  3. Sadhale PP, Woychik NA; , Mol Cell Biol. 1994;14:6164-6170.: C25, an essential RNA polymerase III subunit related to the RNA polymerase II subunit RPB7. PUBMED:8065349 EPMC:8065349

  4. Siaut M, Zaros C, Levivier E, Ferri ML, Court M, Werner M, Callebaut I, Thuriaux P, Sentenac A, Conesa C; , Mol Cell Biol. 2003;23:195-205.: An Rpb4/Rpb7-like complex in yeast RNA polymerase III contains the orthologue of mammalian CGRP-RCP. PUBMED:12482973 EPMC:12482973

  5. Jasiak AJ, Armache KJ, Martens B, Jansen RP, Cramer P; , Mol Cell. 2006;23:71-81.: Structural biology of RNA polymerase III: subcomplex C17/25 X-ray structure and 11 subunit enzyme model. PUBMED:16818233 EPMC:16818233


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005574

This entry includes RNA polymerase II subunit RPB4 and its paralogue, RPC9 (also known as Rpc17 in budding yeasts), a subunit of RNA polymerase III [ PUBMED:12391170 ]. The Rpb4 and Rpb7 subunits of yeast RNA polymerase II form a heterodimeric complex essential for promoter-directed transcription initiation. The Rpb4-Rpb7 complex is not required for stable recruitment of polymerase to active preinitiation complexes, suggesting that Rpb4-Rpb7 mediates an essential step subsequent to promoter binding [ PUBMED:11087726 ]. RPC9 may be involved in the recruitment of pol III by the preinitiation complex [ PUBMED:11433012 , PUBMED:10611227 ].

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 HRDC-like (CL0426), which has the following description:

Superfamily includes HRDC domain from helicases, RNA polymerase II subunit RBP4, RNase D C-terminal domains, and EXOSC10 HRDC domain-like families.

The clan contains the following 5 members:

DNA_pol_A_exoN Helicase_Sgs1 HRDC RNA_pol_Rpb4 UvsW-1

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...

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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
(50)
Full
(3406)
Representative proteomes UniProt
(6870)
RP15
(678)
RP35
(1632)
RP55
(2786)
RP75
(3820)
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PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(50)
Full
(3406)
Representative proteomes UniProt
(6870)
RP15
(678)
RP35
(1632)
RP55
(2786)
RP75
(3820)
Alignment:
Format:
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Sequence:
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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
(50)
Full
(3406)
Representative proteomes UniProt
(6870)
RP15
(678)
RP35
(1632)
RP55
(2786)
RP75
(3820)
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: Finn RD & COG1460
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Bateman A
Number in seed: 50
Number in full: 3406
Average length of the domain: 112.20 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 62.20 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.6 25.6
Trusted cut-off 25.6 25.6
Noise cut-off 25.5 25.5
Model length: 125
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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 RNA_pol_Rpb4 domain has been found. There are 160 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
A0A0R0FCL0 View 3D Structure Click here
A0A0R0IM53 View 3D Structure Click here
A0A0R0ITE8 View 3D Structure Click here
A0A0R0JTM3 View 3D Structure Click here
A0A1D6E557 View 3D Structure Click here
A0A1D6Q9B5 View 3D Structure Click here
A0A1D8PH80 View 3D Structure Click here
A0A1I9LMM7 View 3D Structure Click here
B6SLK8 View 3D Structure Click here
B6SM99 View 3D Structure Click here
B7F9H3 View 3D Structure Click here
C6SV83 View 3D Structure Click here
D4A259 View 3D Structure Click here
F1QK38 View 3D Structure Click here
I1JM88 View 3D Structure Click here
I1K4W5 View 3D Structure Click here
I1L062 View 3D Structure Click here
I1MFU5 View 3D Structure Click here
I1N287 View 3D Structure Click here
K7LRI2 View 3D Structure Click here
K7LVG7 View 3D Structure Click here
K7MPS7 View 3D Structure Click here
K7MSM7 View 3D Structure Click here
K7MSQ7 View 3D Structure Click here
O02092 View 3D Structure Click here
O15514 View 3D Structure Click here
O35427 View 3D Structure Click here
O48890 View 3D Structure Click here
O74825 View 3D Structure Click here
O75575 View 3D Structure Click here
O96150 View 3D Structure Click here
P20433 View 3D Structure Click here
P47076 View 3D Structure Click here
Q0G841 View 3D Structure Click here
Q2QQM6 View 3D Structure Click here
Q54LP2 View 3D Structure Click here
Q54S04 View 3D Structure Click here
Q5AK30 View 3D Structure Click here
Q60351 View 3D Structure Click here
Q6DRG4 View 3D Structure Click here
Q6ZGM1 View 3D Structure Click here
Q7XJ61 View 3D Structure Click here
Q8IM54 View 3D Structure Click here
Q8VHM6 View 3D Structure Click here
Q9C0Z9 View 3D Structure Click here
Q9D7M8 View 3D Structure Click here
Q9VEA5 View 3D Structure Click here
Q9VX99 View 3D Structure Click here