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655  structures 8708  species 0  interactions 13774  sequences 227  architectures

Family: RNA_pol_Rpb2_7 (PF04560)

Summary: RNA polymerase Rpb2, domain 7

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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 7 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 comprised of the structural domains anchor and clamp [1]. The clamp region (C-terminal) contains a zinc-binding motif [1]. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription [1].

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


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007641

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 comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed switch 4. The switches within the polymerase are thought to signal different stages of transcription [ PUBMED:11313498 ].

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
(45)
Full
(13774)
Representative proteomes UniProt
(61646)
RP15
(2477)
RP35
(6870)
RP55
(12783)
RP75
(19915)
Jalview View  View  View  View  View  View  View 
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
(45)
Full
(13774)
Representative proteomes UniProt
(61646)
RP15
(2477)
RP35
(6870)
RP55
(12783)
RP75
(19915)
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
(45)
Full
(13774)
Representative proteomes UniProt
(61646)
RP15
(2477)
RP35
(6870)
RP55
(12783)
RP75
(19915)
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: 45
Number in full: 13774
Average length of the domain: 84.30 aa
Average identity of full alignment: 46 %
Average coverage of the sequence by the domain: 7.13 %

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 32.1 32.1
Trusted cut-off 32.1 32.3
Noise cut-off 31.9 31.9
Model length: 87
Family (HMM) version: 22
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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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_7 domain has been found. There are 655 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
A0A0R0G5J1 View 3D Structure Click here
A0A0R0GQW5 View 3D Structure Click here
A0A0R0L4N1 View 3D Structure Click here
A0A0R4IXL0 View 3D Structure Click here
A0A140KXX5 View 3D Structure Click here
A0A1D6GLH1 View 3D Structure Click here
A0A1D6JFH0 View 3D Structure Click here
A0A1D6KCI0 View 3D Structure Click here
A0A1D6KRW8 View 3D Structure Click here
A0A1D6KX11 View 3D Structure Click here
A0A1D6LJV2 View 3D Structure Click here
A0A1D6LLQ3 View 3D Structure Click here
A0A1D8PQM4 View 3D Structure Click here
A0A1X7YHF8 View 3D Structure Click here
A4I1A3 View 3D Structure Click here
A4I6A8 View 3D Structure Click here
B8JKD7 View 3D Structure Click here
D2WKH8 View 3D Structure Click here
D3ZV30 View 3D Structure Click here
E9AGT7 View 3D Structure Click here
F1QQA2 View 3D Structure Click here
F4I366 View 3D Structure Click here
F4KD38 View 3D Structure Click here
G3V8Y5 View 3D Structure Click here
I1K8M4 View 3D Structure Click here
I1L1L2 View 3D Structure Click here
I1MHA4 View 3D Structure Click here
K7KIE2 View 3D Structure Click here
K7L1D3 View 3D Structure Click here
K7MME1 View 3D Structure Click here
K7TLH8 View 3D Structure Click here
O96236 View 3D Structure Click here
P08266 View 3D Structure Click here
P08518 View 3D Structure Click here
P0A8V2 View 3D Structure Click here
P0C503 View 3D Structure Click here
P16023 View 3D Structure Click here
P20028 View 3D Structure Click here
P21421 View 3D Structure Click here
P22138 View 3D Structure Click here
P22276 View 3D Structure Click here
P25167 View 3D Structure Click here
P30876 View 3D Structure Click here
P38420 View 3D Structure Click here
P47768 View 3D Structure Click here
P50546 View 3D Structure Click here
P59470 View 3D Structure Click here
P70700 View 3D Structure Click here
P9WGY9 View 3D Structure Click here
Q02061 View 3D Structure Click here
Q0J7Q4 View 3D Structure Click here
Q10233 View 3D Structure Click here
Q10578 View 3D Structure Click here
Q10JZ3 View 3D Structure Click here
Q27492 View 3D Structure Click here
Q27493 View 3D Structure Click here
Q4D9P5 View 3D Structure Click here
Q4DWA6 View 3D Structure Click here
Q4E4P5 View 3D Structure Click here
Q54BM1 View 3D Structure Click here
Q54IZ9 View 3D Structure Click here
Q54J75 View 3D Structure Click here
Q59M52 View 3D Structure Click here
Q5A8Y5 View 3D Structure Click here
Q60181 View 3D Structure Click here
Q8CFI7 View 3D Structure Click here
Q8HVY5 View 3D Structure Click here
Q8I5X9 View 3D Structure Click here
Q8II17 View 3D Structure Click here
Q9H9Y6 View 3D Structure Click here
Q9LK40 View 3D Structure Click here
Q9LV32 View 3D Structure Click here
Q9NW08 View 3D Structure Click here
Q9P7X8 View 3D Structure Click here