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137  structures 4471  species 7  interactions 4597  sequences 6  architectures

Family: RNA_pol_Rpb6 (PF01192)

Summary: RNA polymerase Rpb6

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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.

RNA polymerase Rpb6 Provide feedback

Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and III. This family also contains the bacterial equivalent to Rpb6, the omega subunit. Rpb6 and omega are structurally conserved and both function in polymerase assembly [1].

Literature references

  1. Minakhin L, Bhagat S, Brunning A, Campbell EA, Darst SA, Ebright RH, Severinov K; , Proc Natl Acad Sci U S A 2001;98:892-897.: Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly. PUBMED:11158566 EPMC:11158566

  2. Mathew R, Chatterji D; , Trends Microbiol. 2006;14:450-455.: The evolving story of the omega subunit of bacterial RNA polymerase. PUBMED:16908155 EPMC:16908155


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006110

In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. A component of 14 to 18 kDa shared by all three forms of eukaryotic RNA polymerases and which has been sequenced in budding yeast (gene RPB6 or RPO26), in Schizosaccharomyces pombe (Fission yeast) (gene rpb6 or rpo15), in human and in African swine fever virus (ASFV) is evolutionary related to the archaebacterial subunit K (gene rpoK). The archaebacterial protein is colinear with the C-terminal part of the eukaryotic subunit.

The structures of the omega subunit and RBP6, and the structures of the omega/beta' and RPB6/RPB1 interfaces, suggest a molecular mechanism for the function of omega and RPB6 in promoting RNAP assembly and/or stability. The conserved regions of omega and RPB6 form a compact structural domain that interacts simultaneously with conserved regions of the largest RNAP subunit and with the C-terminal tail following a conserved region of the largest RNAP subunit. The second half of the conserved region of omega and RPB6 forms an arc that projects away from the remainder of the structural domain and wraps over and around the C-terminal tail of the largest RNAP subunit, clamping it in a crevice, and threading the C-terminal tail of the largest RNAP subunit through the narrow gap between omega and RPB6 [PUBMED:11158566].

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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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(57)
Full
(4597)
Representative proteomes NCBI
(2396)
Meta
(1900)
RP15
(378)
RP35
(740)
RP55
(987)
RP75
(1177)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(57)
Full
(4597)
Representative proteomes NCBI
(2396)
Meta
(1900)
RP15
(378)
RP35
(740)
RP55
(987)
RP75
(1177)
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
(57)
Full
(4597)
Representative proteomes NCBI
(2396)
Meta
(1900)
RP15
(378)
RP35
(740)
RP55
(987)
RP75
(1177)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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: Family
Author: Finn RD
Number in seed: 57
Number in full: 4597
Average length of the domain: 54.00 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 56.84 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.6 20.6
Trusted cut-off 20.8 20.6
Noise cut-off 20.5 20.5
Model length: 57
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 7 interactions for this family. More...

RNA_pol_Rpb1_3 RNA_pol_Rpb1_1 SHS2_Rpb7-N RNA_pol_Rpb1_5 RNA_pol_Rpb1_6 RNA_pol_Rpb2_7 RNA_pol_Rpb1_2

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_Rpb6 domain has been found. There are 137 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 seqence.

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