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990  structures 8772  species 0  interactions 19647  sequences 251  architectures

Family: RNA_pol_Rpb2_2 (PF04561)

Summary: RNA polymerase Rpb2, domain 2

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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 Rpb2, domain 2 Provide feedback

RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain [1]. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).

Literature references

  1. Cramer P, Bushnell DA, Kornberg RD; , Science 2001;292:1863-1876.: Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. PUBMED:11313498 EPMC:11313498


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007642

RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. It is also known as the lobe domain [ PUBMED:11313498 ]. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, a region known as dispensable region 1 (DRI).

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(22)
Full
(19647)
Representative proteomes UniProt
(98736)
RP15
(3238)
RP35
(9658)
RP55
(18776)
RP75
(30479)
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HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(22)
Full
(19647)
Representative proteomes UniProt
(98736)
RP15
(3238)
RP35
(9658)
RP55
(18776)
RP75
(30479)
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
(22)
Full
(19647)
Representative proteomes UniProt
(98736)
RP15
(3238)
RP35
(9658)
RP55
(18776)
RP75
(30479)
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: Manual
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 22
Number in full: 19647
Average length of the domain: 142.30 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 16.37 %

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 21.7 21.7
Trusted cut-off 21.7 21.7
Noise cut-off 21.6 21.6
Model length: 190
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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

Selections

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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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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_Rpb2_2 domain has been found. There are 990 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
A0A0P0WFD3 View 3D Structure Click here
A0A0P0XVR4 View 3D Structure Click here
A0A0R0G5J1 View 3D Structure Click here
A0A0R0GQW5 View 3D Structure Click here
A0A0R0L4N1 View 3D Structure Click here
A0A0R4IXL0 View 3D Structure Click here
A0A1D6GLH1 View 3D Structure Click here
A0A1D6GRR2 View 3D Structure Click here
A0A1D6JFH0 View 3D Structure Click here
A0A1D6KID2 View 3D Structure Click here
A0A1D6KRW8 View 3D Structure Click here
A0A1D6KX11 View 3D Structure Click here
A0A1D6LJV2 View 3D Structure Click here
A0A1D8PQM4 View 3D Structure Click here
A0A1X7YHF8 View 3D Structure Click here
A0JZ93 View 3D Structure Click here
A0KQA5 View 3D Structure Click here
A0L5W6 View 3D Structure Click here
A0LII4 View 3D Structure Click here
A0LRL3 View 3D Structure Click here
A0PXT8 View 3D Structure Click here
A0T0D7 View 3D Structure Click here
A0T0R1 View 3D Structure Click here
A1A317 View 3D Structure Click here
A1ALT4 View 3D Structure Click here
A1AX75 View 3D Structure Click here
A1B015 View 3D Structure Click here
A1BD23 View 3D Structure Click here
A1E9R4 View 3D Structure Click here
A1KB34 View 3D Structure Click here
A1R8V4 View 3D Structure Click here
A1S211 View 3D Structure Click here
A1SEK1 View 3D Structure Click here
A1T065 View 3D Structure Click here
A1T4J2 View 3D Structure Click here
A1TVT0 View 3D Structure Click here
A1UBJ3 View 3D Structure Click here
A1USC8 View 3D Structure Click here
A1VTF8 View 3D Structure Click here
A1WCM9 View 3D Structure Click here