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- EMDB-5329: Cryo EM reconstruction of mammalian 80S ribosome in rotated PRE s... -

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Basic information

Database: EMDB / ID: 5329
TitleCryo EM reconstruction of mammalian 80S ribosome in rotated PRE state 2
Keywords80S ribosome / mammalian / elongation cycle / tRNA
Sample80S-PRE-rotated-2 complex from rabbit (Oryctolagus cuniculus) liver
SourceOryctolagus cuniculus / mammal / rabbit / アナウサギ /
Map data80S mammalian ribosome
Methodsingle particle reconstruction, at 10.6 Å resolution
AuthorsBudkevich T / Giesebrecht J / Altman R / Munro J / Mielke T / Nierhaus K / Blanchard S / Spahn C
CitationMol. Cell, 2011, 44, 214-224

Mol. Cell, 2011, 44, 214-224 Yorodumi Papers
Structure and dynamics of the mammalian ribosomal pretranslocation complex.
Tatyana Budkevich / Jan Giesebrecht / Roger B Altman / James B Munro / Thorsten Mielke / Knud H Nierhaus / Scott C Blanchard / Christian M T Spahn

Validation ReportPDB-ID: 3j0q

SummaryFull reportAbout validation report
DateDeposition: Jul 12, 2011 / Header (metadata) release: Jul 28, 2011 / Map release: Nov 9, 2011 / Last update: Mar 6, 2013

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 1000
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 1000
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-3j0q
  • Surface level: 1000
  • Imaged by UCSF CHIMERA
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3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_5329.map.gz (map file in CCP4 format, 22783 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
180 pix
2.52 Å/pix.
= 453.6 Å
180 pix
2.52 Å/pix.
= 453.6 Å
180 pix
2.52 Å/pix.
= 453.6 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.52 Å
Contour Level:1000 (by author), 1000 (movie #1):
Minimum - Maximum-2542.37280273 - 17103.23632813
Average (Standard dev.)275.67153931 (1215.57641602)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 453.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.522.522.52
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z453.600453.600453.600
start NX/NY/NZ-62-62-62
MAP C/R/S123
start NC/NR/NS-90-90-89
D min/max/mean-2542.37317103.236275.672

Supplemental data

Sample components

Entire 80S-PRE-rotated-2 complex from rabbit (Oryctolagus cuniculus) liver

EntireName: 80S-PRE-rotated-2 complex from rabbit (Oryctolagus cuniculus) liver
Details: Sample was re-associated from subunits / Number of components: 5 / Oligomeric State: monomer
MassExperimental: 4 MDa / Measured by: Sedimentation

Component #1: ribosome-eukaryote, 80S ribosome

Ribosome-eukaryoteName: 80S ribosome / Eukaryote: LSU 60S, SSU 40S / Recombinant expression: No
MassTheoretical: 4 MDa
SourceSpecies: Oryctolagus cuniculus / mammal / rabbit / アナウサギ /
Source (natural)Organ or tissue: liver

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionpH: 7.5
Support filmQuantifoil grids
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 77 K / Humidity: 100 %
Method: Flash-frozen in liquid ethane on carbon coated Quantifoil grids
Details: Vitrification instrument: VitroBot (FEI)

Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300 / Date: Oct 17, 2006
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 39000 X (nominal), 65520 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 200,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 4000 nm
Specimen HolderHolder: Cartridge / Model: GATAN HELIUM / Temperature: 77 K
CameraDetector: KODAK SO-163 FILM

Image acquisition

Image acquisitionNumber of digital images: 87 / Scanner: PRIMESCAN / Sampling size: 4.7 microns

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 23347
3D reconstructionAlgorithm: Multi-particle refinement / Software: SPIDER / CTF correction: By defocus groups
Details: Several rounds of multireference 3D projection refinement
Resolution: 10.6 Å / Resolution method: FSC 0.5

Atomic model buiding

Output model

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