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- EMDB-1315: Structural basis for interaction of the ribosome with the switch ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1315
TitleStructural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors.
Map dataThis 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 GEF-G
  • RNA: transfer RNA
Function / homology
Function and homology information


translational elongation / translation elongation factor activity / GDP binding / ribosome binding / large ribosomal subunit / regulation of translation / small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome ...translational elongation / translation elongation factor activity / GDP binding / ribosome binding / large ribosomal subunit / regulation of translation / small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / GTP binding / magnesium ion binding / cytoplasm
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 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Elongation factor Tu domain 2 / 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/S23 / Ribosomal protein S12/S23 / Small GTP-binding protein domain / Ribosomal protein S12 signature. / 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 speciesThermus thermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.3 Å
AuthorsConnell SR / Wilson DN / Rost M / Schueler M / Giesebrecht J / Dabrowski M / Mielke T / Fucini P / Spahn CMT
CitationJournal: 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
DepositionJan 18, 2007-
Header (metadata) releaseJan 19, 2007-
Map releaseJan 19, 2008-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3015.196812581
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 3015.196812581
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2om7
  • Surface level: 3015.196812581
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2om7
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1315.gif

Downloads & links

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Map

FileDownload / File: emd_1315.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the volume file of the 70S-EFG-GMPPNP complex from Thermus thermophilus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.26 Å/pix.
x 300 pix.
= 378. Å		1.26 Å/pix.
x 300 pix.
= 378. Å		1.26 Å/pix.
x 300 pix.
= 378. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.26 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1820.0 / Movie #1: 3015.1968126
Minimum - Maximum-4968.550000000000182 - 11069.200000000000728
Average (Standard dev.)-29.847899999999999 (±976.692999999999984)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-150-150-149
Dimensions300300300
Spacing300300300
CellA=B=C: 378 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.261.261.26
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z378.000378.000378.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-150-149
NX/NY/NZ300300300
MAP C/R/S213
start NC/NR/NS-150-150-149
NC/NR/NS300300300
D min/max/mean-4968.55311069.182-29.848

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Supplemental data

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Sample components

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Entire : complex of Thermus thermophilus 70S ribosomes and EF-G-GMPPNP

EntireName: complex of Thermus thermophilus 70S ribosomes and EF-G-GMPPNP
Components
  • Sample: complex of Thermus thermophilus 70S ribosomes and EF-G-GMPPNP
  • Complex: Thermus thermophilus 70S ribosome
  • Protein or peptide: elongation factor GEF-G
  • RNA: transfer RNA

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Supramolecule #1000: complex of Thermus thermophilus 70S ribosomes and EF-G-GMPPNP

SupramoleculeName: complex of Thermus thermophilus 70S ribosomes and EF-G-GMPPNP
type: sample / ID: 1000 / Number unique components: 3

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Supramolecule #1: Thermus thermophilus 70S ribosome

SupramoleculeName: Thermus thermophilus 70S ribosome / type: complex / ID: 1 / Ribosome-details: ribosome-prokaryote: ALL

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Macromolecule #1: elongation factor G

MacromoleculeName: elongation factor G / type: protein_or_peptide / ID: 1 / Name.synonym: EF-G / Recombinant expression: Yes
Source (natural)Organism: Thermus thermophilus (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21DE3

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Macromolecule #2: transfer RNA

MacromoleculeName: transfer RNA / type: rna / ID: 2 / Name.synonym: tRNA / Classification: TRANSFER / Structure: OTHER / Synthetic?: No
Source (natural)Organism: Thermus thermophilus (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
Details: 0.3 mM GMPPNP, 10 mM Hepes-KOH (pH 7.8), 10 mM Mg acetate, 60 mM NH4Cl, and 6 mM B-mercaptoethanol
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 4 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 39000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Number real images: 371 / Average electron dose: 19 e/Å2
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: defocus groups
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 77038

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Atomic model buiding 1

SoftwareName: Situs
DetailsProtocol: Rigid Body
RefinementProtocol: RIGID BODY FIT
Output model

PDB-2om7:
Structural Basis for Interaction of the Ribosome with the Switch Regions of GTP-bound Elongation Factors

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