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- EMDB-38669: State 7 (S7) of yeast 80S ribosome bound to 2 tRNAs and eEF2 duri... -

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Basic information

Entry
Database: EMDB / ID: EMD-38669
TitleState 7 (S7) of yeast 80S ribosome bound to 2 tRNAs and eEF2 during tranlocation
Map data
Sample
  • Complex: Yeast 80S ribosome
Keywords80S / elongation cycle / rotated / translocation / TRANSLATION
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsCheng J / Wu CL / Li JX / Zhang XZ
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930069 China
National Natural Science Foundation of China (NSFC)32150010 China
Chinese Academy of SciencesXDB37040101 China
CitationJournal: To Be Published
Title: Snapshots of ribosome dynamics near atomic resolution in situ: a full insight into eukaryotic elongation cycle
Authors: Cheng J / Wu CL / Li JX / Yang Q / Zhao MJ / Zhang XZ
History
DepositionJan 12, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38669.png

Downloads & links

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Map

FileDownload / File: emd_38669.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 400 pix.
= 528. Å		1.32 Å/pix.
x 400 pix.
= 528. Å		1.32 Å/pix.
x 400 pix.
= 528. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.29
Minimum - Maximum-0.6250219 - 1.3129208
Average (Standard dev.)0.0005650362 (±0.07574283)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 528.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38669_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38669_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38669_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Yeast 80S ribosome

EntireName: Yeast 80S ribosome
Components
  • Complex: Yeast 80S ribosome

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Supramolecule #1: Yeast 80S ribosome

SupramoleculeName: Yeast 80S ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#80
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: BY4741

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 4.5 / Details: YPD
VitrificationCryogen name: ETHANE / Chamber humidity: 90 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16956
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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