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Yorodumi- EMDB-5174: Structure of 70S ribosome in the 100S ribosome in the hibernation... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5174 | |||||||||
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Title | Structure of 70S ribosome in the 100S ribosome in the hibernation stage | |||||||||
Map data | The density map of 70S ribosome with part of its partner in the 100S ribosome in hibernation stage. | |||||||||
Sample |
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Keywords | cryoelectron microscopy / ribosomal protein | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 18.0 Å | |||||||||
Authors | Kato T / Yoshida H / Miyata T / Maki Y / Wada A / Namba K | |||||||||
Citation | Journal: Structure / Year: 2010 Title: Structure of the 100S ribosome in the hibernation stage revealed by electron cryomicroscopy. Authors: Takayuki Kato / Hideji Yoshida / Tomoko Miyata / Yasushi Maki / Akira Wada / Keiichi Namba / Abstract: In the stationary growth phase of bacteria, protein biosynthesis on ribosomes is suppressed, and the ribosomes are preserved in the cell by the formation of the 100S ribosome. The 100S ribosome is a ...In the stationary growth phase of bacteria, protein biosynthesis on ribosomes is suppressed, and the ribosomes are preserved in the cell by the formation of the 100S ribosome. The 100S ribosome is a dimer of the 70S ribosome and is formed by the binding of the ribosome modulation factor and the hibernation promoting factor. However, the binding mode between the two 70S ribosomes and the mechanism of complex formation are still poorly understood. Here, we report the structure of the 100S ribosome by electron cryomicroscopy and single-particle image analysis. The 100S ribosome purified from the cell in the stationary growth phase is composed of two transfer RNA-free 70S ribosomes, has two-fold symmetry, and is formed through interactions between their 30S subunits, where interactions between small subunit proteins, S2, S3 and S5, appear to be critical for the dimerization. | |||||||||
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_5174.map.gz | 59.5 MB | EMDB map data format | |
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Header (meta data) | emd-5174-v30.xml emd-5174.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | emd_5174.png emd_5174_1.png | 132 KB 139.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5174 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5174 | HTTPS FTP |
-Validation report
Summary document | emd_5174_validation.pdf.gz | 78.1 KB | Display | EMDB validaton report |
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Full document | emd_5174_full_validation.pdf.gz | 77.2 KB | Display | |
Data in XML | emd_5174_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5174 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5174 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5174.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The density map of 70S ribosome with part of its partner in the 100S ribosome in hibernation stage. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.69 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 100S ribosome
Entire | Name: E. coli 100S ribosome |
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Components |
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-Supramolecule #1000: E. coli 100S ribosome
Supramolecule | Name: E. coli 100S ribosome / type: sample / ID: 1000 Details: The 100S ribosome was fixed by GraFix with glutaraldehyde. Oligomeric state: dimer of 70S ribosome / Number unique components: 1 |
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-Supramolecule #1: 100S ribosome
Supramolecule | Name: 100S 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) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 / Details: 20 mM HEPES-KCL, 77 mM KCl, 15 mM (CH3COO)2Mg |
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Grid | Details: Quantifoil 0.6/1 on 200 mesh molybdenum grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 100 K / Instrument: OTHER / Details: Vitrification instrument: FEI Vitrobot / Method: Blot for 7 seconds before plunging |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Temperature | Min: 50 K / Max: 70 K |
Specialist optics | Energy filter - Name: JEOL Omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 10.0 eV |
Date | Feb 25, 2009 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 300 / Average electron dose: 20 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 88760 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.6 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Top entry liquid helium-cooled cryo specimen holder Specimen holder model: JEOL |
-Image processing
Details | Each of the two 70S ribosome particle images with part of the dimer pair was extracted in a box with circler mask from 100S ribosome particle image. |
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CTF correction | Details: Each particle |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 17461 |
Final two d classification | Number classes: 552 |