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Yorodumi- EMDB-5796: Structure of the Ribosome with Elongation Factor G Trapped in the... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5796 | |||||||||
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Title | Structure of the Ribosome with Elongation Factor G Trapped in the Pre-Translocation State | |||||||||
Map data | 70S ribosome with A, P and E tRNA (Class I) | |||||||||
Sample |
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Keywords | protein structure / translation / EF-G / electron cryo-microscopy / single particle analysis | |||||||||
Biological species | Escherichia coli (E. coli) / synthetic construct (others) / unidentified (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.9 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5796.map.gz | 102.6 MB | EMDB map data format | |
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Header (meta data) | emd-5796-v30.xml emd-5796.xml | 12.7 KB 12.7 KB | Display Display | EMDB header |
Images | emd_5796_1.jpg emd_5796_2.png | 236.4 KB 232.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5796 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5796 | HTTPS FTP |
-Validation report
Summary document | emd_5796_validation.pdf.gz | 78.3 KB | Display | EMDB validaton report |
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Full document | emd_5796_full_validation.pdf.gz | 77.4 KB | Display | |
Data in XML | emd_5796_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5796 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5796 | HTTPS FTP |
-Related structure data
Related structure data | 5797C 5798C 5799C 5800C 4v7cC 4v7dC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5796.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 70S ribosome with A, P and E tRNA (Class I) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Ribosome with A, P, E sites occupied by tRNA
Entire | Name: Ribosome with A, P, E sites occupied by tRNA |
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Components |
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-Supramolecule #1000: Ribosome with A, P, E sites occupied by tRNA
Supramolecule | Name: Ribosome with A, P, E sites occupied by tRNA / type: sample / ID: 1000 / Details: Sample was monodisperse / Number unique components: 4 |
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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 |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: MRE600 |
Molecular weight | Theoretical: 3 MDa |
-Macromolecule #1: Transfer RNA
Macromolecule | Name: Transfer RNA / type: rna / ID: 1 / Name.synonym: tRNA / Details: Three tRNA present (A, P and E sites). / Classification: TRANSFER / Structure: DOUBLE HELIX / Synthetic?: No |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: K-12 |
Molecular weight | Experimental: 25 KDa |
-Macromolecule #2: Messenger RNA
Macromolecule | Name: Messenger RNA / type: rna / ID: 2 / Name.synonym: mRNA / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 12 KDa |
Sequence | String: GGCAAGGAGG UAAAAAUGUU UAAACGUAAA UCUACU |
-Macromolecule #3: Viomycin
Macromolecule | Name: Viomycin / type: ligand / ID: 3 / Name.synonym: Vio / Number of copies: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 1 KDa |
Chemical component information |
ChemComp-PRD_000226: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL |
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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 |
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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. |
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CTF correction | Details: CTFFIND3, FREALIGN per micrograph |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 5.9 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: 356854 |