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- EMDB-5174: Structure of 70S ribosome in the 100S ribosome in the hibernation... -

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Basic information

Entry
Database: EMDB / ID: EMD-5174
TitleStructure of 70S ribosome in the 100S ribosome in the hibernation stage
Map dataThe density map of 70S ribosome with part of its partner in the 100S ribosome in hibernation stage.
Sample
  • Sample: E. coli 100S ribosome
  • Complex: 100S ribosome
Keywordscryoelectron microscopy / ribosomal protein
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 18.0 Å
AuthorsKato T / Yoshida H / Miyata T / Maki Y / Wada A / Namba K
CitationJournal: 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
DepositionMar 10, 2010-
Header (metadata) releaseApr 23, 2010-
Map releaseOct 19, 2010-
UpdateMar 6, 2013-
Current statusMar 6, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5174.png

emd_5174_1.png

Downloads & links

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Map

FileDownload / File: emd_5174.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe density map of 70S ribosome with part of its partner in the 100S ribosome in hibernation stage.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.69 Å/pix.
x 256 pix.
= 432.64 Å		1.69 Å/pix.
x 256 pix.
= 432.64 Å		1.69 Å/pix.
x 256 pix.
= 432.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-4.61667633 - 7.85508204
Average (Standard dev.)0.00009336 (±0.86218983)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 432.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.691.691.69
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z432.640432.640432.640
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-4.6177.8550.000

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Supplemental data

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Sample components

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Entire : E. coli 100S ribosome

EntireName: E. coli 100S ribosome
Components
  • Sample: E. coli 100S ribosome
  • Complex: 100S ribosome

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Supramolecule #1000: E. coli 100S ribosome

SupramoleculeName: 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

SupramoleculeName: 100S ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6 / Details: 20 mM HEPES-KCL, 77 mM KCl, 15 mM (CH3COO)2Mg
GridDetails: Quantifoil 0.6/1 on 200 mesh molybdenum grid
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 100 K / Instrument: OTHER / Details: Vitrification instrument: FEI Vitrobot / Method: Blot for 7 seconds before plunging

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Electron microscopy

MicroscopeJEOL 3200FSC
TemperatureMin: 50 K / Max: 70 K
Specialist opticsEnergy filter - Name: JEOL Omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 10.0 eV
DateFeb 25, 2009
Image recordingCategory: 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 beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated 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 stageSpecimen holder: Top entry liquid helium-cooled cryo specimen holder
Specimen holder model: JEOL

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Image processing

DetailsEach 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.
CTF correctionDetails: Each particle
Final reconstructionAlgorithm: 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 classificationNumber classes: 552

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