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- EMDB-38659: State 2b (S2b) of yeast 80S ribosome bound to 2 tRNAs during pept... -

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Basic information

Entry
Database: EMDB / ID: EMD-38659
TitleState 2b (S2b) of yeast 80S ribosome bound to 2 tRNAs during peptidyl transfer
Map data
Sample
  • Complex: Yeast 80S ribosome
Keywords80S / elongation cycle / rotated / peptidyl transfer / TRANSLATION
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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: Nat Struct Mol Biol / Year: 2025
Title: Capturing eukaryotic ribosome dynamics in situ at high resolution.
Authors: Jing Cheng / Chunling Wu / Junxi Li / Qi Yang / Mingjie Zhao / Xinzheng Zhang /
Abstract: Many protein complexes are highly dynamic in cells; thus, characterizing their conformational changes in cells is crucial for unraveling their functions. Here, using cryo-electron microscopy, 451,700 ...Many protein complexes are highly dynamic in cells; thus, characterizing their conformational changes in cells is crucial for unraveling their functions. Here, using cryo-electron microscopy, 451,700 ribosome particles from Saccharomyces cerevisiae cell lamellae were obtained to solve the 60S region to 2.9-Å resolution by in situ single-particle analysis. Over 20 distinct conformations were identified by three-dimensional classification with resolutions typically higher than 4 Å. These conformations were used to reconstruct a complete elongation cycle of eukaryotic translation with elongation factors (eEFs). We found that compact eEF2 anchors to the partially rotated ribosome after subunit rolling and hypothesize that it stabilizes the local conformation for peptidyl transfer. Moreover, open-eEF3 binding to a fully rotated ribosome was observed, whose conformational change was coupled with head swiveling and body back-rotation of the 40S subunit.
History
DepositionJan 12, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38659.png

Downloads & links

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Map

FileDownload / File: emd_38659.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.335
Minimum - Maximum-1.5215024 - 2.5105894
Average (Standard dev.)0.00016148397 (±0.10720708)
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_38659_msk_1.map
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Half map: #2

Fileemd_38659_half_map_1.map
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Half map: #1

Fileemd_38659_half_map_2.map
Projections & Slices
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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
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

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57852
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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