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- EMDB-65471: 40S ribosome subunit of HeLa cell treated by sodium arsenite -

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Basic information

Entry
Database: EMDB / ID: EMD-65471
Title40S ribosome subunit of HeLa cell treated by sodium arsenite
Map data
Sample
  • Cell: HeLa cells treated by sodium arsenite
Keywordsribosome / stress granules / sodium arsenite
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 11.0 Å
AuthorsYichun W / Xing W
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2025
Title: Translation landscape of stress granules.
Authors: Yichun Wu / Xing Wang / Lingyu Meng / Zhizhao Liao / Wei Ji / Peipei Zhang / Jie Lin / Qiang Guo /
Abstract: Stress granules, cytoplasmic assemblies of RNA binding proteins and messenger RNAs formed during cellular stress, are implicated in translational control. However, their exact functions remain ...Stress granules, cytoplasmic assemblies of RNA binding proteins and messenger RNAs formed during cellular stress, are implicated in translational control. However, their exact functions remain elusive. Here, we used cryogenic correlative light and electron microscopy to visualize stress granules in their native environment and reconstructed them in three dimensions using tomography. This approach provided the first quantitative and spatial analysis of the translational machinery within stress granules. Our findings suggest that stress granules have a limited impact on global translation regulation but serve to protect small ribosomal subunits and preinitiation complexes from degradation. Numerical simulations based on a phase-field model accurately reproduced the spatial distribution of ribosomal components inside and outside the stress granules, shedding light on the thermodynamic principles governing this process.
History
DepositionJul 21, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65471.png

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Map

FileDownload / File: emd_65471.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
2.74 Å/pix.
x 200 pix.
= 548. Å		2.74 Å/pix.
x 200 pix.
= 548. Å		2.74 Å/pix.
x 200 pix.
= 548. Å

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Voxel sizeX=Y=Z: 2.74 Å
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Contour LevelBy AUTHOR: 0.496
Minimum - Maximum-0.44973472 - 1.4936476
Average (Standard dev.)0.009476475 (±0.08203462)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 548.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65471_msk_1.map
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Half map: #1

Fileemd_65471_half_map_1.map
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Half map: #2

Fileemd_65471_half_map_2.map
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Sample components

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Entire : HeLa cells treated by sodium arsenite

EntireName: HeLa cells treated by sodium arsenite
Components
  • Cell: HeLa cells treated by sodium arsenite

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Supramolecule #1: HeLa cells treated by sodium arsenite

SupramoleculeName: HeLa cells treated by sodium arsenite / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.35 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 4400
ExtractionNumber tomograms: 67 / Number images used: 4400 / Software - Name: PyTom
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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