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- EMDB-1342: Structures of modified eEF2 80S ribosome complexes reveal the rol... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1342 | |||||||||
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Title | Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation. | |||||||||
![]() | Cryo-EM map of 80S ribosome bound with eEF2 | |||||||||
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Function / homology | ![]() Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / Protein methylation / translational elongation / translation elongation factor activity / Neutrophil degranulation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / maintenance of translational fidelity / ribosome binding ...Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / Protein methylation / translational elongation / translation elongation factor activity / Neutrophil degranulation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / maintenance of translational fidelity / ribosome binding / protein-folding chaperone binding / rRNA binding / ribonucleoprotein complex / GTPase activity / GTP binding / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 11.3 Å | |||||||||
![]() | Taylor DJ / Nilsson J / Merrill AR / Andersen GR / Nissen P / Frank J | |||||||||
![]() | ![]() Title: Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation. Authors: Derek J Taylor / Jakob Nilsson / A Rod Merrill / Gregers Rom Andersen / Poul Nissen / Joachim Frank / ![]() Abstract: On the basis of kinetic data on ribosome protein synthesis, the mechanical energy for translocation of the mRNA-tRNA complex is thought to be provided by GTP hydrolysis of an elongation factor (eEF2 ...On the basis of kinetic data on ribosome protein synthesis, the mechanical energy for translocation of the mRNA-tRNA complex is thought to be provided by GTP hydrolysis of an elongation factor (eEF2 in eukaryotes, EF-G in bacteria). We have obtained cryo-EM reconstructions of eukaryotic ribosomes complexed with ADP-ribosylated eEF2 (ADPR-eEF2), before and after GTP hydrolysis, providing a structural basis for analyzing the GTPase-coupled mechanism of translocation. Using the ADP-ribosyl group as a distinct marker, we observe conformational changes of ADPR-eEF2 that are due strictly to GTP hydrolysis. These movements are likely representative of native eEF2 motions in a physiological context and are sufficient to uncouple the mRNA-tRNA complex from two universally conserved bases in the ribosomal decoding center (A1492 and A1493 in Escherichia coli) during translocation. Interpretation of these data provides a detailed two-step model of translocation that begins with the eEF2/EF-G binding-induced ratcheting motion of the small ribosomal subunit. GTP hydrolysis then uncouples the mRNA-tRNA complex from the decoding center so translocation of the mRNA-tRNA moiety may be completed by a head rotation of the small subunit. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 30.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.7 KB 10.7 KB | Display Display | ![]() |
Images | ![]() | 73 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2p8wMC ![]() 1343C ![]() 1344C ![]() 1345C ![]() 2p8xC ![]() 2p8yC ![]() 2p8zC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cryo-EM map of 80S ribosome bound with eEF2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.86 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Thermomyces lanuginosus 80S ribosome
Entire | Name: Thermomyces lanuginosus 80S ribosome |
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Components |
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-Supramolecule #1000: Thermomyces lanuginosus 80S ribosome
Supramolecule | Name: Thermomyces lanuginosus 80S ribosome / type: sample / ID: 1000 / Number unique components: 3 |
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Molecular weight | Theoretical: 3.0 MDa |
-Supramolecule #1: Thermomyces lanuginosus
Supramolecule | Name: Thermomyces lanuginosus / type: complex / ID: 1 / Ribosome-details: ribosome-eukaryote: ALL |
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Molecular weight | Experimental: 3.0 MDa |
-Macromolecule #1: eEF2
Macromolecule | Name: eEF2 / type: protein_or_peptide / ID: 1 / Recombinant expression: No |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 93 KDa |
-Macromolecule #2: tRNA
Macromolecule | Name: tRNA / type: rna / ID: 2 / Classification: TRANSFER / Structure: SINGLE STRANDED / Synthetic?: No |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 / Details: see Methods |
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Staining | Type: NEGATIVE / Details: No staining (Cryo-EM) |
Grid | Details: Quanti-foil grids coated with a thin carbon layer |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 279 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot Method: Apply sample, wait 30s, blot for 6s, plunge in liquid ethane |
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Electron microscopy
Microscope | FEI TECNAI F30 |
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Temperature | Average: 84 K |
Date | Jul 7, 2005 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 93 / Average electron dose: 25 e/Å2 / Bits/pixel: 12 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 37642 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 4.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 39000 |
Sample stage | Specimen holder: cartridge / Specimen holder model: OTHER |
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: CTF correction of 3D map |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.3 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER package / Number images used: 93807 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: RSRef2.0 |
Details | PDBEntryID_givenInChain. Protocol: Rigid Body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 15 / Target criteria: cross-correlation |
Output model | ![]() PDB-2p8w: |