[English] 日本語
Yorodumi- EMDB-5797: Structure of the Ribosome with Elongation Factor G Trapped in the... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5797 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the Ribosome with Elongation Factor G Trapped in the Pre-Translocation State | |||||||||
Map data | Ribosome reconstruction | |||||||||
Sample |
| |||||||||
Keywords | protein structure / translation / EF-G / electron cryo-microscopy / single particle analysis | |||||||||
Function / homology | Function and homology information intracellular anatomical structure / ribosome disassembly / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / synthetic construct (others) / unidentified (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.2 Å | |||||||||
Authors | Brilot AF / Korostelev AA / Ermolenko DN / Grigorieff N | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2013 Title: Structure of the ribosome with elongation factor G trapped in the pretranslocation state. Authors: Axel F Brilot / Andrei A Korostelev / Dmitri N Ermolenko / Nikolaus Grigorieff / Abstract: During protein synthesis, tRNAs and their associated mRNA codons move sequentially on the ribosome from the A (aminoacyl) site to the P (peptidyl) site to the E (exit) site in a process catalyzed by ...During protein synthesis, tRNAs and their associated mRNA codons move sequentially on the ribosome from the A (aminoacyl) site to the P (peptidyl) site to the E (exit) site in a process catalyzed by a universally conserved ribosome-dependent GTPase [elongation factor G (EF-G) in prokaryotes and elongation factor 2 (EF-2) in eukaryotes]. Although the high-resolution structure of EF-G bound to the posttranslocation ribosome has been determined, the pretranslocation conformation of the ribosome bound with EF-G and A-site tRNA has evaded visualization owing to the transient nature of this state. Here we use electron cryomicroscopy to determine the structure of the 70S ribosome with EF-G, which is trapped in the pretranslocation state using antibiotic viomycin. Comparison with the posttranslocation ribosome shows that the small subunit of the pretranslocation ribosome is rotated by ∼12° relative to the large subunit. Domain IV of EF-G is positioned in the cleft between the body and head of the small subunit outwardly of the A site and contacts the A-site tRNA. Our findings suggest a model in which domain IV of EF-G promotes the translocation of tRNA from the A to the P site as the small ribosome subunit spontaneously rotates back from the hybrid, rotated state into the nonrotated posttranslocation state. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5797.map.gz | 105.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-5797-v30.xml emd-5797.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
Images | emd_5797_1.jpg emd_5797_2.png | 224.6 KB 236.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5797 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5797 | HTTPS FTP |
-Validation report
Summary document | emd_5797_validation.pdf.gz | 78.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_5797_full_validation.pdf.gz | 77.3 KB | Display | |
Data in XML | emd_5797_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5797 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5797 | HTTPS FTP |
-Related structure data
Related structure data | 5796C 5798C 5799C 5800C 4v7cC 4v7dC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_5797.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Ribosome reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Post-translocation ribosome bound to EF-G with P, E sites occupie...
Entire | Name: Post-translocation ribosome bound to EF-G with P, E sites occupied by tRNA |
---|---|
Components |
|
-Supramolecule #1000: Post-translocation ribosome bound to EF-G with P, E sites occupie...
Supramolecule | Name: Post-translocation ribosome bound to EF-G with P, E sites occupied by tRNA type: sample / ID: 1000 / Details: Sample was monodisperse / Number unique components: 6 |
---|---|
Molecular weight | Theoretical: 3 MDa |
-Supramolecule #1: 70S ribosome
Supramolecule | Name: 70S ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-prokaryote: ALL |
---|---|
Source (natural) | Organism: Escherichia coli (E. coli) / Strain: MRE600 |
Molecular weight | Theoretical: 3 MDa |
-Macromolecule #1: Elongation Factor G
Macromolecule | Name: Elongation Factor G / type: protein_or_peptide / ID: 1 / Name.synonym: EF-G / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Escherichia coli (E. coli) / Strain: K-12 |
Molecular weight | Theoretical: 78 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: K-12 |
Sequence | UniProtKB: Elongation factor G GO: translational elongation, GTP binding, translation elongation factor activity, intracellular anatomical structure InterPro: Translation elongation factor EFG/EF2 |
-Macromolecule #2: Transfer RNA
Macromolecule | Name: Transfer RNA / type: rna / ID: 2 / Name.synonym: tRNA / Details: Two tRNA present (P and E sites). / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No |
---|---|
Source (natural) | Organism: Escherichia coli (E. coli) / Strain: K-12 |
Molecular weight | Experimental: 25 KDa |
-Macromolecule #3: Messenger RNA
Macromolecule | Name: Messenger RNA / type: rna / ID: 3 / Name.synonym: mRNA / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 12 KDa |
Sequence | String: GGCAAGGAGG UAAAAAUGUU UAAACGUAAA UCUACU |
-Macromolecule #4: Fusidic Acid
Macromolecule | Name: Fusidic Acid / type: ligand / ID: 4 / Name.synonym: Fus / Number of copies: 1 / Recombinant expression: No / Database: NCBI |
---|---|
Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 1 KDa |
Chemical component information | ChemComp-FUA: |
-Macromolecule #5: Viomycin
Macromolecule | Name: Viomycin / type: ligand / ID: 5 / Name.synonym: Vio / Number of copies: 1 / Recombinant expression: No / Database: NCBI |
---|---|
Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 1 KDa |
Chemical component information |
ChemComp-PRD_000226: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL |
---|---|
Buffer | pH: 7.6 Details: 10 mM HEPES-KOH, 5 mM MgCl2, 90 mM NH4Cl, 2 mM spermidine, 0.1 mM spermine, 6 mM BME, 0.5 mM viomycin, 0.5 mM GTP, 0.5 mM fusidic acid |
Grid | Details: C-flat 1.2/1.3 holey carbon 400 mesh copper grid, glow discharged with a current of -20 mA for 45 seconds in an EMITECH K100X glow discharge unit |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK II Method: Freshly glow-disharged grids were loaded into an FEI Mark II Vitrobot and equilibrated to 95% relative humidity at 22 degrees Celsius. 2 microliters of sample was applied through the side ...Method: Freshly glow-disharged grids were loaded into an FEI Mark II Vitrobot and equilibrated to 95% relative humidity at 22 degrees Celsius. 2 microliters of sample was applied through the side port, blotted for 7 seconds with a positional offset of 2, and plunged into liquid ethane. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Alignment procedure | Legacy - Astigmatism: Automatically corrected using FEI software |
Date | Nov 2, 2012 |
Image recording | Category: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Digitization - Sampling interval: 14.0 µm / Number real images: 13341 / Average electron dose: 30 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 134615 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 6.95 µm / Nominal defocus min: 1.15 µm / Nominal magnification: 133333 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | Refinement and 3D classification performed by Frealign. See primary citation Supplementary Information for details. |
---|---|
CTF correction | Details: CTFFIND3, FREALIGN per micrograph |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: OTHER / Software - Name: EMAN2, IMAGIC, FREALIGN, RSAMPLE, CTFFIND3 Details: Refinement included data to 12 Angstrom resolution to limit FSC bias. See primary citation Supplementary Information for details. Number images used: 1341961 |