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Yorodumi- EMDB-1324: Spontaneous reverse movement of mRNA-bound tRNA through the ribosome. -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1324 | |||||||||
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Title | Spontaneous reverse movement of mRNA-bound tRNA through the ribosome. | |||||||||
Map data | none | |||||||||
Sample |
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Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.0 Å | |||||||||
Authors | Konevega AL / Fischer N / Semenkov YP / Stark H / Wintermeyer W / Rodnina MV | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2007 Title: Spontaneous reverse movement of mRNA-bound tRNA through the ribosome. Authors: Andrey L Konevega / Niels Fischer / Yuri P Semenkov / Holger Stark / Wolfgang Wintermeyer / Marina V Rodnina / Abstract: During the translocation step of protein synthesis, a complex of two transfer RNAs bound to messenger RNA (tRNA-mRNA) moves through the ribosome. The reaction is promoted by an elongation factor, ...During the translocation step of protein synthesis, a complex of two transfer RNAs bound to messenger RNA (tRNA-mRNA) moves through the ribosome. The reaction is promoted by an elongation factor, called EF-G in bacteria, which, powered by GTP hydrolysis, induces an open, unlocked conformation of the ribosome that allows for spontaneous tRNA-mRNA movement. Here we show that, in the absence of EF-G, there is spontaneous backward movement, or retrotranslocation, of two tRNAs bound to mRNA. Retrotranslocation is driven by the gain in affinity when a cognate E-site tRNA moves into the P site, which compensates the affinity loss accompanying the movement of peptidyl-tRNA from the P to the A site. These results lend support to the diffusion model of tRNA movement during translocation. In the cell, tRNA movement is biased in the forward direction by EF-G, which acts as a Brownian ratchet and prevents backward movement. | |||||||||
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_1324.map.gz | 7.5 MB | EMDB map data format | |
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Header (meta data) | emd-1324-v30.xml emd-1324.xml | 7.7 KB 7.7 KB | Display Display | EMDB header |
Images | 1324.gif | 54 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1324 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1324 | HTTPS FTP |
-Related 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_1324.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | none | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 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 : E. Coli 70S-tRNA complex prior to retrotranslocation 70S-fMetVal-...
Entire | Name: E. Coli 70S-tRNA complex prior to retrotranslocation 70S-fMetVal-tRNAVal |
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Components |
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-Supramolecule #1000: E. Coli 70S-tRNA complex prior to retrotranslocation 70S-fMetVal-...
Supramolecule | Name: E. Coli 70S-tRNA complex prior to retrotranslocation 70S-fMetVal-tRNAVal type: sample / ID: 1000 / Number unique components: 2 |
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-Supramolecule #1: E. Coli 70S
Supramolecule | Name: E. Coli 70S / type: complex / ID: 1 / Ribosome-details: ribosome-prokaryote: ALL |
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-Macromolecule #1: fMet-Val-tRNAVal
Macromolecule | Name: fMet-Val-tRNAVal / type: rna / ID: 1 / Classification: TRANSFER / Structure: OTHER / Synthetic?: No |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Details: 50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine. |
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Grid | Details: 200 mesh copper grid |
Vitrification | Cryogen name: ETHANE / Method: Manual blotting |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 166000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Image recording | Category: CCD / Film or detector model: GENERIC TVIPS (4k x 4k) / Average electron dose: 19 e/Å2 |
-Image processing
CTF correction | Details: local |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: OTHER / Software - Name: Imagic / Number images used: 11732 |
Details | Particles selected semiautomatically. |