- EMDB-1315: Structural basis for interaction of the ribosome with the switch ... -
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Basic information
Entry
Database: EMDB / ID: EMD-1315
Title
Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors.
Map data
This is the volume file of the 70S-EFG-GMPPNP complex from Thermus thermophilus
Sample
Sample: complex of Thermus thermophilus 70S ribosomes and EF-G-GMPPNP
Complex: Thermus thermophilus 70S ribosome
Protein or peptide: elongation factor G
RNA: transfer RNA
Function / homology
Function and homology information
ribosome disassembly / translational elongation / translation elongation factor activity / GDP binding / ribosome binding / regulation of translation / small ribosomal subunit / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding ...ribosome disassembly / translational elongation / translation elongation factor activity / GDP binding / ribosome binding / regulation of translation / small ribosomal subunit / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / GTP binding / magnesium ion binding / cytosol Similarity search - Function
: / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L1, bacterial-type / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV ...: / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L1, bacterial-type / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S12, bacterial-type / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S12 signature. / Small GTP-binding protein domain / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase Similarity search - Domain/homology
Elongation factor G / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS12 / Elongation factor G / Large ribosomal subunit protein uL1 Similarity search - Component
Biological species
Thermus thermophilus (bacteria)
Method
single particle reconstruction / cryo EM / Resolution: 7.3 Å
Journal: Mol Cell / Year: 2007 Title: Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors. Authors: Sean R Connell / Chie Takemoto / Daniel N Wilson / Hongfei Wang / Kazutaka Murayama / Takaho Terada / Mikako Shirouzu / Maximilian Rost / Martin Schüler / Jan Giesebrecht / Marylena ...Authors: Sean R Connell / Chie Takemoto / Daniel N Wilson / Hongfei Wang / Kazutaka Murayama / Takaho Terada / Mikako Shirouzu / Maximilian Rost / Martin Schüler / Jan Giesebrecht / Marylena Dabrowski / Thorsten Mielke / Paola Fucini / Shigeyuki Yokoyama / Christian M T Spahn / Abstract: Elongation factor G (EF-G) catalyzes tRNA translocation on the ribosome. Here a cryo-EM reconstruction of the 70S*EF-G ribosomal complex at 7.3 A resolution and the crystal structure of EF-G-2*GTP, ...Elongation factor G (EF-G) catalyzes tRNA translocation on the ribosome. Here a cryo-EM reconstruction of the 70S*EF-G ribosomal complex at 7.3 A resolution and the crystal structure of EF-G-2*GTP, an EF-G homolog, at 2.2 A resolution are presented. EF-G-2*GTP is structurally distinct from previous EF-G structures, and in the context of the cryo-EM structure, the conformational changes are associated with ribosome binding and activation of the GTP binding pocket. The P loop and switch II approach A2660-A2662 in helix 95 of the 23S rRNA, indicating an important role for these conserved bases. Furthermore, the ordering of the functionally important switch I and II regions, which interact with the bound GTP, is dependent on interactions with the ribosome in the ratcheted conformation. Therefore, a network of interaction with the ribosome establishes the active GTP conformation of EF-G and thus facilitates GTP hydrolysis and tRNA translocation.
History
Deposition
Jan 18, 2007
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Header (metadata) release
Jan 19, 2007
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Map release
Jan 19, 2008
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Update
May 26, 2011
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Current status
May 26, 2011
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Number real images: 371 / Average electron dose: 19 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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