|Entry||Database: EMDB / ID: 5329|
|Title||Cryo EM reconstruction of mammalian 80S ribosome in rotated PRE state 2|
|Keywords||80S ribosome / mammalian / elongation cycle / tRNA|
|Sample||80S-PRE-rotated-2 complex from rabbit (Oryctolagus cuniculus) liver|
|Source||Oryctolagus cuniculus / mammal / rabbit / アナウサギ /|
|Map data||80S mammalian ribosome|
|Method||single particle reconstruction, at 10.6 Å resolution|
|Authors||Budkevich T / Giesebrecht J / Altman R / Munro J / Mielke T / Nierhaus K / Blanchard S / Spahn C|
|Citation||Mol. Cell, 2011, 44, 214-224|
|Validation Report||PDB-ID: 3j0q|
SummaryFull reportAbout validation report
|Date||Deposition: Jul 12, 2011 / Header (metadata) release: Jul 28, 2011 / Map release: Nov 9, 2011 / Last update: Mar 6, 2013|
Downloads & links
|File||emd_5329.map.gz (map file in CCP4 format, 22783 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.52 Å|
CCP4 map header:
-Entire 80S-PRE-rotated-2 complex from rabbit (Oryctolagus cuniculus) liver
|Entire||Name: 80S-PRE-rotated-2 complex from rabbit (Oryctolagus cuniculus) liver|
Details: Sample was re-associated from subunits / Number of components: 5 / Oligomeric State: monomer
|Mass||Experimental: 4 MDa / Measured by: Sedimentation|
-Component #1: ribosome-eukaryote, 80S ribosome
|Ribosome-eukaryote||Name: 80S ribosome / Eukaryote: LSU 60S, SSU 40S / Recombinant expression: No|
|Mass||Theoretical: 4 MDa|
|Source||Species: Oryctolagus cuniculus / mammal / rabbit / アナウサギ /|
|Source (natural)||Organ or tissue: liver|
|Sample solution||pH: 7.5|
|Support film||Quantifoil grids|
|Vitrification||Instrument: 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
Model: Tecnai Polara / Image courtesy: FEI Company
|Imaging||Microscope: FEI POLARA 300 / Date: Oct 17, 2006|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: SPOT SCAN|
|Lens||Magnification: 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 Holder||Holder: Cartridge / Model: GATAN HELIUM / Temperature: 77 K|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 87 / Scanner: PRIMESCAN / Sampling size: 4.7 microns|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 23347|
|3D reconstruction||Algorithm: 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
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