Summary: Elongation factor Tu C-terminal domain
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This is the Wikipedia entry entitled "GTP-binding elongation factor family, EF-Tu/EF-1A subfamily". More...
GTP-binding elongation factor family, EF-Tu/EF-1A subfamily Edit Wikipedia article
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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
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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
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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
SCOOP: | GTP_EFTU |
External database links
SCOP: | 1etu |
This tab holds annotation information from the InterPro database.
InterPro entry IPR004160
Elongation factor EF1A (also known as EF-1alpha or EF-Tu) promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. EF1A consists of three structural domains. Release factor eRF3, which governs translation termination, has a similar overall structure. RF3 has an N-terminal extension and a EF1A-like C-terminal region which comprises a GTP-binding domain (G domain) and two beta-barrel domains that are similar to the three respective domains of elongation factor EF-Tu/eEF1A [PUBMED:10676813]. Archaeal EF1A is both involved in translational elongation and termination, as well as in mRNA surveillance, which explains the lack of an eRF3 orthologue in archaea [PUBMED:20974926].
This entry represents the C-terminal domain of both EF1A and eRF3, which adopts a beta-barrel structure. In EF1A, this domain 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 (50) |
Full (15921) |
Representative proteomes | UniProt (88934) |
NCBI (92586) |
Meta (2590) |
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RP15 (2353) |
RP35 (7317) |
RP55 (13848) |
RP75 (22094) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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Seed (50) |
Full (15921) |
Representative proteomes | UniProt (88934) |
NCBI (92586) |
Meta (2590) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (2353) |
RP35 (7317) |
RP55 (13848) |
RP75 (22094) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | PF00009 |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 50 |
Number in full: | 15921 |
Average length of the domain: | 98.30 aa |
Average identity of full alignment: | 38 % |
Average coverage of the sequence by the domain: | 22.12 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 108 | ||||||||||||
Family (HMM) version: | 18 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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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Interactions
There are 15 interactions for this family. More...
MHC_II_beta RNA_replicase_B SmpB MHC_II_alpha GTP_EFTU EF_TS eRF1_3 EF_TS GTP_EFTU_D3 GTP_EFTU GTP_EFTU_D2 eRF1_3 GTP_EFTU_D2 eRF1_2 EF1_GNEStructures
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 196 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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