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194  structures 8710  species 0  interactions 20575  sequences 180  architectures

Family: EFG_IV (PF03764)

Summary: Elongation factor G, domain IV

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Elongation factor G, domain IV Provide feedback

This domain is found in elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopts a ribosomal protein S5 domain 2-like fold.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005517

Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [ PUBMED:12762045 , PUBMED:15922593 , PUBMED:12932732 ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution.

Elongation factor EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position [ PUBMED:12762009 , PUBMED:12762047 ]. This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome.

EF2 has five domains. This entry represents domain IV found in EF2 (or EF-G) of both prokaryotes and eukaryotes. The EF2-GTP-ribosome complex undergoes extensive structural rearrangement for tRNA-mRNA movement to occur. Domain IV, which extends from the 'body' of the EF2 molecule much like a lever arm, facilitates the movement of peptidyl-tRNA from the A to the P site, being critical for the structural transition to take place [ PUBMED:25288752 ].

Included in this entry is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins that is homologous to domain IV of EF-G. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA [ PUBMED:11735030 , PUBMED:1935960 , PUBMED:15922593 , PUBMED:1602493 , PUBMED:8159735 , PUBMED:10837219 , PUBMED:12471894 , PUBMED:16213500 , PUBMED:12932345 ].

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 S5 (CL0329), which has the following description:

This superfamily contains a wide range of families that possess a structure similar to the second domain of ribosomal S5 protein.

The clan contains the following 18 members:

ChlI DNA_gyraseB DNA_mis_repair EFG_IV Fae GalKase_gal_bdg GHMP_kinases_N IGPD Lon_C LpxC Morc6_S5 Ribonuclease_P Ribosomal_S5_C Ribosomal_S9 RNase_PH Topo-VIb_trans UPF0029 Xol-1_N

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
(64)
Full
(20575)
Representative proteomes UniProt
(80155)
RP15
(3376)
RP35
(10250)
RP55
(19575)
RP75
(31185)
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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
(64)
Full
(20575)
Representative proteomes UniProt
(80155)
RP15
(3376)
RP35
(10250)
RP55
(19575)
RP75
(31185)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(64)
Full
(20575)
Representative proteomes UniProt
(80155)
RP15
(3376)
RP35
(10250)
RP55
(19575)
RP75
(31185)
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: Pfam-B_40 (release 2.1)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Griffiths-Jones SR
Number in seed: 64
Number in full: 20575
Average length of the domain: 118.70 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 16.25 %

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 24.0 24.0
Noise cut-off 23.9 23.9
Model length: 121
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 EFG_IV domain has been found. There are 194 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
A0A096QR66 View 3D Structure Click here
A0A1D6E4M0 View 3D Structure Click here
A0A1D6I3L1 View 3D Structure Click here
A0A1D6LAW0 View 3D Structure Click here
A0A1D6P3B9 View 3D Structure Click here
A0A1D8PH71 View 3D Structure Click here
A0A286Y8X9 View 3D Structure Click here
A0JMI9 View 3D Structure Click here
A2CE51 View 3D Structure Click here
A4I1Q6 View 3D Structure Click here
A4I843 View 3D Structure Click here
A4ICS8 View 3D Structure Click here
A4ICW8 View 3D Structure Click here
B6U0S1 View 3D Structure Click here
C6KSM4 View 3D Structure Click here
C6KSM4 View 3D Structure Click here
F1LM66 View 3D Structure Click here
F1Q6N0 View 3D Structure Click here
F4IW10 View 3D Structure Click here
F4JB05 View 3D Structure Click here
F4JWP9 View 3D Structure Click here
I1J6F0 View 3D Structure Click here
I1K0K6 View 3D Structure Click here
I1KU21 View 3D Structure Click here
I1LZW4 View 3D Structure Click here
I1MJ86 View 3D Structure Click here
I1MTZ8 View 3D Structure Click here
K7MDZ1 View 3D Structure Click here
K7UKK5 View 3D Structure Click here
O08810 View 3D Structure Click here
O14460 View 3D Structure Click here
O94316 View 3D Structure Click here
P05197 View 3D Structure Click here
P0A6M8 View 3D Structure Click here
P13060 View 3D Structure Click here
P13639 View 3D Structure Click here
P15112 View 3D Structure Click here
P25039 View 3D Structure Click here
P29691 View 3D Structure Click here
P32324 View 3D Structure Click here
P34811 View 3D Structure Click here
P36048 View 3D Structure Click here
P58252 View 3D Structure Click here
P9WNM7 View 3D Structure Click here
P9WNM9 View 3D Structure Click here
Q07803 View 3D Structure Click here
Q08BB1 View 3D Structure Click here
Q0JBE3 View 3D Structure Click here
Q15029 View 3D Structure Click here
Q1LYG5 View 3D Structure Click here
Q1LYG6 View 3D Structure Click here
Q23463 View 3D Structure Click here
Q2G0N1 View 3D Structure Click here
Q4CUP9 View 3D Structure Click here
Q4CWR1 View 3D Structure Click here
Q4CXN3 View 3D Structure Click here
Q4D3T1 View 3D Structure Click here
Q4D5X0 View 3D Structure Click here
Q4DDK0 View 3D Structure Click here
Q4DGU6 View 3D Structure Click here
Q54JK7 View 3D Structure Click here
Q54JV1 View 3D Structure Click here
Q54R72 View 3D Structure Click here
Q55E94 View 3D Structure Click here
Q55G92 View 3D Structure Click here
Q58448 View 3D Structure Click here
Q5A0M4 View 3D Structure Click here
Q5AL45 View 3D Structure Click here
Q5BJP6 View 3D Structure Click here
Q5JKU5 View 3D Structure Click here
Q69V60 View 3D Structure Click here
Q6H4L2 View 3D Structure Click here
Q7XTK1 View 3D Structure Click here
Q8I592 View 3D Structure Click here
Q8IJZ9 View 3D Structure Click here
Q8IKW5 View 3D Structure Click here
Q8K0D5 View 3D Structure Click here
Q8R2Q4 View 3D Structure Click here
Q8W0C4 View 3D Structure Click here
Q95Y73 View 3D Structure Click here
Q969S9 View 3D Structure Click here
Q96RP9 View 3D Structure Click here
Q9ASR1 View 3D Structure Click here
Q9C641 View 3D Structure Click here
Q9FE64 View 3D Structure Click here
Q9LNC5 View 3D Structure Click here
Q9SI75 View 3D Structure Click here
Q9USZ1 View 3D Structure Click here
Q9VAX8 View 3D Structure Click here
Q9VM33 View 3D Structure Click here
Q9XV52 View 3D Structure Click here