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- EMDB-30554: Cryo-EM structure of disome from saccharomyces cerevisiae, the tr... -

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Basic information

Entry
Database: EMDB / ID: EMD-30554
TitleCryo-EM structure of disome from saccharomyces cerevisiae, the trailing ribosome in the rotated state with A/P and P/E tRNAs
Map dataCryo-EM structure of disome from saccharomyces cerevisiae, the colliding ribosome in the rotated state with A/P and P/E tRNAs
Sample
  • Complex: Cryo-EM structure of disome from saccharomyces cerevisiae, the leading ribosome in the rotated state with A/P and P/E tRNAs
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.85 Å
AuthorsYu L / Taolan Z / Yanming C
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900455, 91331112, 31725007, 31630087 China
CitationJournal: To Be Published
Title: Cryo-EM structure of disome from saccharomyces cerevisiae, the trailing ribosome in the rotated state with A/P and P/E tRNAs
Authors: Yu L / Taolan Z / Yanming C
History
DepositionSep 19, 2020-
Header (metadata) releaseDec 23, 2020-
Map releaseDec 23, 2020-
UpdateDec 23, 2020-
Current statusDec 23, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.005
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.005
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30554.png

Downloads & links

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Map

FileDownload / File: emd_30554.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of disome from saccharomyces cerevisiae, the colliding ribosome in the rotated state with A/P and P/E tRNAs
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 440 pix.
= 596.64 Å		1.36 Å/pix.
x 440 pix.
= 596.64 Å		1.36 Å/pix.
x 440 pix.
= 596.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.356 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.005
Minimum - Maximum-0.010112218 - 0.028328402
Average (Standard dev.)6.303756e-05 (±0.0020104926)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 596.63995 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3561.3561.356
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z596.640596.640596.640
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.0100.0280.000

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of disome from saccharomyces cerevisiae, the le...

EntireName: Cryo-EM structure of disome from saccharomyces cerevisiae, the leading ribosome in the rotated state with A/P and P/E tRNAs
Components
  • Complex: Cryo-EM structure of disome from saccharomyces cerevisiae, the leading ribosome in the rotated state with A/P and P/E tRNAs

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Supramolecule #1: Cryo-EM structure of disome from saccharomyces cerevisiae, the le...

SupramoleculeName: Cryo-EM structure of disome from saccharomyces cerevisiae, the leading ribosome in the rotated state with A/P and P/E tRNAs
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 34.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

4427

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27599
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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