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107  structures 8481  species 0  interactions 25002  sequences 127  architectures

Family: RF-1 (PF00472)

Summary: RF-1 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.

RF-1 domain Provide feedback

This domain is found in peptide chain release factors such as RF-1 (P07011) and RF-2 (P07012), and a number of smaller proteins of unknown function such as P40711. This domain contains the peptidyl-tRNA hydrolase activity. The domain contains a highly conserved motif GGQ, where the glutamine is thought to coordinate the water that mediates the hydrolysis.

Literature references

  1. Song H, Mugnier P, Das AK, Webb HM, Evans DR, Tuite MF, Hemmings BA, Barford D; , Cell 2000;100:311-321.: The crystal structure of human eukaryotic release factor eRF1--mechanism of stop codon recognition and peptidyl-tRNA hydrolysis. PUBMED:10676813 EPMC:10676813


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000352

Peptide chain release factors (RFs) are required for the termination of protein biosynthesis [ PUBMED:8821264 ]. At present two classes of RFs can be distinguished. Class I RFs bind to ribosomes that have encountered a stop codon at their decoding site and induce release of the nascent polypeptide. Class II RFs are GTP-binding proteins that interact with class I RFs and enhance class I RF activity. In prokaryotes there are two class I RFs that act in a codon specific manner [ PUBMED:2215213 ]: RF-1(gene prfA) mediates UAA and UAG-dependent termination while RF-2 (gene prfB) mediates UAA and UGA-dependent termination. RF-1 and RF-2 are structurally and evolutionary related proteins which have been shown to be part of a larger family [ PUBMED:1408743 ].

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 RF (CL0337), which has the following description:

These families are peptide chain release factors.

The clan contains the following 2 members:

MRP-S28 RF-1

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
(802)
Full
(25002)
Representative proteomes UniProt
(105235)
RP15
(3634)
RP35
(12085)
RP55
(24363)
RP75
(40442)
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
(802)
Full
(25002)
Representative proteomes UniProt
(105235)
RP15
(3634)
RP35
(12085)
RP55
(24363)
RP75
(40442)
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
(802)
Full
(25002)
Representative proteomes UniProt
(105235)
RP15
(3634)
RP35
(12085)
RP55
(24363)
RP75
(40442)
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: Prosite
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A , Finn RD
Number in seed: 802
Number in full: 25002
Average length of the domain: 114.50 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 37.30 %

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 35.0 35.0
Trusted cut-off 35.0 35.0
Noise cut-off 34.8 34.9
Model length: 116
Family (HMM) version: 22
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 RF-1 domain has been found. There are 107 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
A0A0P0VBA3 View 3D Structure Click here
A0A0R0EZV4 View 3D Structure Click here
A0A0R0FT17 View 3D Structure Click here
A0A0R0KN35 View 3D Structure Click here
A0A0R0KY84 View 3D Structure Click here
A0A143ZXY8 View 3D Structure Click here
A0A1D6E418 View 3D Structure Click here
A0A1D6F6J5 View 3D Structure Click here
A0A1D6FLB1 View 3D Structure Click here
A0A1D6FMZ2 View 3D Structure Click here
A0A1D6HMT7 View 3D Structure Click here
A0A1D6IEG8 View 3D Structure Click here
A0A1D6JW26 View 3D Structure Click here
A0A1D6LBM0 View 3D Structure Click here
A0A1D6LF60 View 3D Structure Click here
A0A1D6LF61 View 3D Structure Click here
A0A1D6ML41 View 3D Structure Click here
A0A1D6N598 View 3D Structure Click here
A0A1D6PP97 View 3D Structure Click here
A0A1D8PLX1 View 3D Structure Click here
A0A1Q0ZZU5 View 3D Structure Click here
A1ZAD7 View 3D Structure Click here
A2RVR7 View 3D Structure Click here
A4HZC8 View 3D Structure Click here
A4I1J1 View 3D Structure Click here
A4I5D7 View 3D Structure Click here
A5WUX7 View 3D Structure Click here
B4G0P4 View 3D Structure Click here
D3ZDP2 View 3D Structure Click here
E5QCJ3 View 3D Structure Click here
E7F0D0 View 3D Structure Click here
F1LWN5 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
I1K0H7 View 3D Structure Click here
I1L681 View 3D Structure Click here
I1LA53 View 3D Structure Click here
I1MUU5 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
P28369 View 3D Structure Click here
P30775 View 3D Structure Click here
P40711 View 3D Structure Click here
P9WHG1 View 3D Structure Click here
P9WHG3 View 3D Structure Click here
Q05863 View 3D Structure Click here
Q09691 View 3D Structure Click here
Q10MK3 View 3D Structure Click here
Q10P29 View 3D Structure Click here
Q12322 View 3D Structure Click here
Q14197 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
Q4D0W9 View 3D Structure Click here
Q4DG05 View 3D Structure Click here
Q4DIB4 View 3D Structure Click here
Q4DX82 View 3D Structure Click here
Q4E0T8 View 3D Structure Click here
Q4E1T2 View 3D Structure Click here
Q4V7E5 View 3D Structure Click here
Q54IC8 View 3D Structure Click here
Q54RE7 View 3D Structure Click here
Q59P48 View 3D Structure Click here
Q5A2B6 View 3D Structure Click here
Q80VP5 View 3D Structure Click here
Q84JF2 View 3D Structure Click here
Q86JL2 View 3D Structure Click here
Q8BJU9 View 3D Structure Click here
Q8GVY3 View 3D Structure Click here
Q8I1W0 View 3D Structure Click here
Q8I2J2 View 3D Structure Click here
Q8IC21 View 3D Structure Click here
Q8IIJ1 View 3D Structure Click here
Q8ILH8 View 3D Structure Click here
Q8K126 View 3D Structure Click here
Q8R035 View 3D Structure Click here
Q8RX79 View 3D Structure Click here
Q95QC2 View 3D Structure Click here
Q9C875 View 3D Structure Click here
Q9H3J6 View 3D Structure Click here
Q9HDZ3 View 3D Structure Click here
Q9LVY0 View 3D Structure Click here
Q9UGC7 View 3D Structure Click here
Q9VK20 View 3D Structure Click here
Q9VKU3 View 3D Structure Click here
Q9Y811 View 3D Structure Click here