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64  structures 491  species 5  interactions 1033  sequences 19  architectures

Family: SHS2_Rpb7-N (PF03876)

Summary: SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397

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SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 Provide feedback

Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II [1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA [2]. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction [3].

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. Yuan X, Zhao J, Zentgraf H, Hoffmann-Rohrer U, Grummt I; , 0;0:1-2.: Multiple interactions between RNA polymerase I, TIF-IA and TAFI subunits regulate preinitiation complex assembly at the ribosomal gene promoter. PUBMED:12393749 EPMC:12393749

  3. Anantharaman V, Aravind L;, Proteins. 2004;56:795-807.: The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies. PUBMED:15281131 EPMC:15281131


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005576

The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [PUBMED:11741548].

This entry represents the N-terminal, heterodimerisation domain of RPB7.

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 SHS2 (CL0319), which contains the following 7 members:

Archease Cass2 Dodecin GyrI-like SHS2_FTSA SHS2_Rpb7-N SOUL

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...

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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
(145)
Full
(1033)
Representative proteomes NCBI
(949)
Meta
(87)
RP15
(224)
RP35
(387)
RP55
(571)
RP75
(703)
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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
(145)
Full
(1033)
Representative proteomes NCBI
(949)
Meta
(87)
RP15
(224)
RP35
(387)
RP55
(571)
RP75
(703)
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
(145)
Full
(1033)
Representative proteomes NCBI
(949)
Meta
(87)
RP15
(224)
RP35
(387)
RP55
(571)
RP75
(703)
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.

Pfam alignments:

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: Hand
Previous IDs: RNA_pol_Rpb7_N;
Type: Domain
Author: Finn RD, Anantharaman V
Number in seed: 145
Number in full: 1033
Average length of the domain: 71.80 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 30.62 %

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 20.9 20.9
Trusted cut-off 20.9 21.0
Noise cut-off 20.5 20.7
Model length: 70
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 5 interactions for this family. More...

RNA_pol_Rpb2_7 RNA_pol_Rpb1_2 RNA_pol_Rpb6 S1 RNA_pol_Rpb4

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 SHS2_Rpb7-N domain has been found. There are 64 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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