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195  structures 9065  species 15  interactions 16121  sequences 164  architectures

Family: GTP_EFTU_D3 (PF03143)

Summary: Elongation factor Tu C-terminal domain

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Elongation factor Tu C-terminal domain Provide feedback

Elongation factor Tu consists of three structural domains, this is the third domain. This domain adopts a beta barrel structure. This the third domain is involved in binding to both charged tRNA [1] and binding to EF-Ts PF00889 [2].

Literature references

  1. Nissen P, Kjeldgaard M, Thirup S, Polekhina G, Reshetnikova L, Clark BF, Nyborg J; , Science 1995;270:1464-1472.: Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. PUBMED:7491491 EPMC:7491491

  2. Wang Y, Jiang Y, Meyering-Voss M, Sprinzl M, Sigler PB; , Nat Struct Biol 1997;4:650-656.: Crystal structure of the EF-Tu.EF-Ts complex from Thermus thermophilus. PUBMED:9253415 EPMC:9253415


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004160

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.

EF1A (also known as EF-1alpha or EF-Tu) is a G-protein. It forms a ternary complex of EF1A-GTP-aminoacyltRNA. The binding of aminoacyl-tRNA stimulates GTP hydrolysis by EF1A, causing a conformational change in EF1A that causes EF1A-GDP to detach from the ribosome, leaving the aminoacyl-tRNA attached at the A-site. Only the cognate aminoacyl-tRNA can induce the required conformational change in EF1A through its tight anticodon-codon binding [PUBMED:15680978, PUBMED:12102560]. EF1A-GDP is returned to its active state, EF1A-GTP, through the action of another elongation factor, EF1B (also known as EF-Ts or EF-1beta/gamma/delta).

EF1A consists of three structural domains. This entry represents the C-terminal domain, which adopts a beta-barrel structure, and is involved in binding to both charged tRNA and to EF1B (or EF-Ts, INTERPRO) [PUBMED:9253415].

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, the UniProtKB sequence database, 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
(53)
Full
(16121)
Representative proteomes UniProt
(67739)
NCBI
(69028)
Meta
(2586)
RP15
(4362)
RP35
(10016)
RP55
(14417)
RP75
(19229)
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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
(53)
Full
(16121)
Representative proteomes UniProt
(67739)
NCBI
(69028)
Meta
(2586)
RP15
(4362)
RP35
(10016)
RP55
(14417)
RP75
(19229)
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
(53)
Full
(16121)
Representative proteomes UniProt
(67739)
NCBI
(69028)
Meta
(2586)
RP15
(4362)
RP35
(10016)
RP55
(14417)
RP75
(19229)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: PF00009
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 53
Number in full: 16121
Average length of the domain: 97.90 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 22.68 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.7 7.1
Trusted cut-off 24.7 7.9
Noise cut-off 24.6 7.0
Model length: 112
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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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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Interactions

There are 15 interactions for this family. More...

RNA_replicase_B EF1_GNE MHC_II_beta GTP_EFTU_D2 MHC_II_alpha SmpB eRF1_3 GTP_EFTU GTP_EFTU_D3 GTP_EFTU EF_TS GTP_EFTU_D2 eRF1_2 eRF1_3 EF_TS

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 GTP_EFTU_D3 domain has been found. There are 195 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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