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50  structures 1849  species 0  interactions 4540  sequences 72  architectures

Family: eRF1_2 (PF03464)

Summary: eRF1 domain 2

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eRF1 domain 2 Provide feedback

The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known [1]. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site [1]. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.

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 IPR005141

This domain is found in the release factor eRF1 which terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known [ PUBMED:10676813 ]. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site [ PUBMED:10676813 ].

This domain is also found in other proteins which may also be involved in translation termination

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 S11_L18p (CL0267), which has the following description:

This superfamily includes two ribosomal proteins S11 and L18p as well as a domain from eukaryotic peptide chain release factor. This superfamily is likely to share an RNA-binding function.

The clan contains the following 17 members:

acVLRF1 baeRF_family10 baeRF_family11 baeRF_family12 baeRF_family2 baeRF_family3 baeRF_family5 baeRF_family6 baeRF_family7 baeRF_family8 bVLRF1 eRF1_1 eRF1_2 Host_attach Ribosomal_L18p Ribosomal_L5e Ribosomal_S11

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...

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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
(21)
Full
(4540)
Representative proteomes UniProt
(10426)
RP15
(940)
RP35
(2163)
RP55
(3646)
RP75
(5060)
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PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(21)
Full
(4540)
Representative proteomes UniProt
(10426)
RP15
(940)
RP35
(2163)
RP55
(3646)
RP75
(5060)
Alignment:
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Sequence:
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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
(21)
Full
(4540)
Representative proteomes UniProt
(10426)
RP15
(940)
RP35
(2163)
RP55
(3646)
RP75
(5060)
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: Bateman A
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 21
Number in full: 4540
Average length of the domain: 129.90 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 31.08 %

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 27.1 27.1
Trusted cut-off 27.1 27.1
Noise cut-off 27.0 27.0
Model length: 133
Family (HMM) version: 18
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 eRF1_2 domain has been found. There are 50 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
A0A0R0FLB4 View 3D Structure Click here
A0A0R0I9D1 View 3D Structure Click here
A0A0R4IPP6 View 3D Structure Click here
A0A1D6DVD9 View 3D Structure Click here
A0A1D6M1D4 View 3D Structure Click here
A0A1D6ML83 View 3D Structure Click here
A0A1D8PSD0 View 3D Structure Click here
A0A2R8QI78 View 3D Structure Click here
A4I1V7 View 3D Structure Click here
A4I2W3 View 3D Structure Click here
B4FQK5 View 3D Structure Click here
B6U1I9 View 3D Structure Click here
I1JD21 View 3D Structure Click here
I1LBV2 View 3D Structure Click here
I1MNR1 View 3D Structure Click here
I1MQJ9 View 3D Structure Click here
I1NIJ9 View 3D Structure Click here
K7MXQ6 View 3D Structure Click here
O16520 View 3D Structure Click here
O96203 View 3D Structure Click here
P12385 View 3D Structure Click here
P33309 View 3D Structure Click here
P35614 View 3D Structure Click here
P48612 View 3D Structure Click here
P50444 View 3D Structure Click here
P62495 View 3D Structure Click here
P79063 View 3D Structure Click here
Q39097 View 3D Structure Click here
Q4DP00 View 3D Structure Click here
Q4DP89 View 3D Structure Click here
Q4DVM1 View 3D Structure Click here
Q54VC8 View 3D Structure Click here
Q57638 View 3D Structure Click here
Q58239 View 3D Structure Click here
Q59ZH8 View 3D Structure Click here
Q5U2Q7 View 3D Structure Click here
Q5XIP1 View 3D Structure Click here
Q6ZIQ1 View 3D Structure Click here
Q75I90 View 3D Structure Click here
Q75K79 View 3D Structure Click here