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66  structures 8408  species 0  interactions 18013  sequences 84  architectures

Family: PCRF (PF03462)

Summary: PCRF domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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.

PCRF domain Provide feedback

This domain is found in peptide chain release factors.

Literature references

  1. Korostelev A, Asahara H, Lancaster L, Laurberg M, Hirschi A, Zhu J, Trakhanov S, Scott WG, Noller HF;, Proc Natl Acad Sci U S A. 2008;105:19684-19689.: Crystal structure of a translation termination complex formed with release factor RF2. PUBMED:19064930 EPMC:19064930


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005139

This domain is found in bacterial, mitochondrial and chloroplastic peptide chain release factors. In bacteria, termination of protein synthesis depends on the type I release factors, RF1 and RF2 [ PUBMED:2215213 ]. Both contain this domain.

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
(870)
Full
(18013)
Representative proteomes UniProt
(79455)
RP15
(2696)
RP35
(8992)
RP55
(17813)
RP75
(29411)
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
(870)
Full
(18013)
Representative proteomes UniProt
(79455)
RP15
(2696)
RP35
(8992)
RP55
(17813)
RP75
(29411)
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
(870)
Full
(18013)
Representative proteomes UniProt
(79455)
RP15
(2696)
RP35
(8992)
RP55
(17813)
RP75
(29411)
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: Dlakic M
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Dlakic M
Number in seed: 870
Number in full: 18013
Average length of the domain: 185.20 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 51.20 %

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 24.0 24.0
Trusted cut-off 24.1 24.0
Noise cut-off 23.9 23.9
Model length: 192
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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 PCRF domain has been found. There are 66 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
A0A0R0EZV4 View 3D Structure Click here
A0A0R0KN35 View 3D Structure Click here
A0A0R0KN35 View 3D Structure Click here
A0A0R0KY84 View 3D Structure Click here
A0A1D6E418 View 3D Structure Click here
A0A1D6FLB1 View 3D Structure Click here
A0A1D6HMT7 View 3D Structure Click here
A0A1D6IEG8 View 3D Structure Click here
A0A1D6J1Q9 View 3D Structure Click here
A0A1D6J1R0 View 3D Structure Click here
A0A1D6LF60 View 3D Structure Click here
A0A1D6LF61 View 3D Structure Click here
A0A1D6M2W7 View 3D Structure Click here
A0A1D6ML41 View 3D Structure Click here
A0A1D6PP97 View 3D Structure Click here
A0A1D8PLX1 View 3D Structure Click here
A0A1Q0ZZU5 View 3D Structure Click here
A2RVR7 View 3D Structure Click here
A4I1J1 View 3D Structure Click here
B4G0P4 View 3D Structure Click here
F1QA94 View 3D Structure Click here
F1QCR1 View 3D Structure Click here
F4I532 View 3D Structure Click here
F4J264 View 3D Structure Click here
I1JK72 View 3D Structure Click here
I1JQI6 View 3D Structure Click here
I1L681 View 3D Structure Click here
I1LA53 View 3D Structure Click here
I1NB26 View 3D Structure Click here
K7KGK6 View 3D Structure Click here
K7MZU2 View 3D Structure Click here
M0RDC8 View 3D Structure Click here
O44568 View 3D Structure Click here
O75570 View 3D Structure Click here
P07012 View 3D Structure Click here
P0A7I0 View 3D Structure Click here
P30775 View 3D Structure Click here
P9WHG1 View 3D Structure Click here
P9WHG3 View 3D Structure Click here
Q09691 View 3D Structure Click here
Q10MK3 View 3D Structure Click here
Q2FWE0 View 3D Structure Click here
Q2G052 View 3D Structure Click here
Q2R068 View 3D Structure Click here
Q4CKH0 View 3D Structure Click here
Q4DIB4 View 3D Structure Click here
Q4V7E5 View 3D Structure Click here
Q54IC8 View 3D Structure Click here
Q54RE7 View 3D Structure Click here
Q8BJU9 View 3D Structure Click here
Q8GVY3 View 3D Structure Click here
Q8I2J2 View 3D Structure Click here
Q8IC21 View 3D Structure Click here
Q8ILH8 View 3D Structure Click here
Q8K126 View 3D Structure Click here
Q8RX79 View 3D Structure Click here
Q9LVY0 View 3D Structure Click here
Q9UGC7 View 3D Structure Click here
Q9VK20 View 3D Structure Click here