[English] 日本語
Yorodumi- EMDB-1553: Pretranslocation ribosome. Group after ML3D classification. Rache... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1553 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Pretranslocation ribosome. Group after ML3D classification. Racheted ribosome with tRNAs in hybrid positions. | |||||||||
Map data | Racheted ribosome with tRNAs in hybrid positions. | |||||||||
Sample |
| |||||||||
Keywords | ribosome / pretranslocation / hybrid | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 16.0 Å | |||||||||
Authors | Julian P / Konevega AL / Scheres SHW / Lazaro M / Gil D / Wintermeyer W / Rodnina MV / Valle M | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2008 Title: Structure of ratcheted ribosomes with tRNAs in hybrid states. Authors: Patricia Julián / Andrey L Konevega / Sjors H W Scheres / Melisa Lázaro / David Gil / Wolfgang Wintermeyer / Marina V Rodnina / Mikel Valle / Abstract: During protein synthesis, tRNAs and mRNA move through the ribosome between aminoacyl (A), peptidyl (P), and exit (E) sites of the ribosome in a process called translocation. Translocation is ...During protein synthesis, tRNAs and mRNA move through the ribosome between aminoacyl (A), peptidyl (P), and exit (E) sites of the ribosome in a process called translocation. Translocation is accompanied by the displacement of the tRNAs on the large ribosomal subunit toward the hybrid A/P and P/E states and by a rotational movement (ratchet) of the ribosomal subunits relative to one another. So far, the structure of the ratcheted state has been observed only when translation factors were bound to the ribosome. Using cryo-electron microscopy and classification, we show here that ribosomes can spontaneously adopt a ratcheted conformation with tRNAs in their hybrid states. The peptidyl-tRNA molecule in the A/P state, which is visualized here, is not distorted compared with the A/A state except for slight adjustments of its acceptor end, suggesting that the displacement of the A-site tRNA on the 50S subunit is passive and is induced by the 30S subunit rotation. Simultaneous subunit ratchet and formation of the tRNA hybrid states precede and may promote the subsequent rapid and coordinated tRNA translocation on the 30S subunit catalyzed by elongation factor G. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1553.map.gz | 14.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-1553-v30.xml emd-1553.xml | 8.4 KB 8.4 KB | Display Display | EMDB header |
Images | emd_1553.jpg | 59.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1553 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1553 | HTTPS FTP |
-Validation report
Summary document | emd_1553_validation.pdf.gz | 233.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_1553_full_validation.pdf.gz | 232.9 KB | Display | |
Data in XML | emd_1553_validation.xml.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1553 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1553 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_1553.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Racheted ribosome with tRNAs in hybrid positions. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : 70 mRNA tRNAfMet fMetLeu-tRNALeu
Entire | Name: 70 mRNA tRNAfMet fMetLeu-tRNALeu |
---|---|
Components |
|
-Supramolecule #1000: 70 mRNA tRNAfMet fMetLeu-tRNALeu
Supramolecule | Name: 70 mRNA tRNAfMet fMetLeu-tRNALeu / type: sample / ID: 1000 / Number unique components: 3 |
---|
-Supramolecule #1: 70S E.coli ribosome in the pretranslocation state
Supramolecule | Name: 70S E.coli ribosome in the pretranslocation state / type: complex / ID: 1 / Name.synonym: pretranslocation ribosome / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL |
---|---|
Source (natural) | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Details: 50 mM Tris-HCl, pH 7.5 30mM KCl 70 mM NH4Cl 20 mM MgCl2 2 mM spermine |
---|---|
Staining | Type: NEGATIVE / Details: cryoEM |
Grid | Details: Quantifoil 300 mesh copper |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: single blot for 1.5 seconds |
-Electron microscopy
Microscope | JEOL 2200FS |
---|---|
Temperature | Average: 90 K |
Image recording | Category: CCD / Film or detector model: GENERIC GATAN / Digitization - Sampling interval: 2.2 µm / Average electron dose: 10 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm |
Sample stage | Specimen holder: single tilt cryoholder / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: volume |
---|---|
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: OTHER / Software - Name: SPIDER XMIPP / Details: subset after ML3D classification / Number images used: 12590 |