[English] 日本語
Yorodumi
- EMDB-65460: 80S ribosome class 2 with eEF2 in unrotated state of HeLa cell tr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-65460
Title80S ribosome class 2 with eEF2 in unrotated state 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: 9.9 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

-
Structure visualization

Supplemental images

emd_65460.png

Downloads & links

-
Map

FileDownload / File: emd_65460.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.634
Minimum - Maximum-0.96984786 - 2.184384
Average (Standard dev.)0.012401401 (±0.18967697)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #1

Fileemd_65460_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_65460_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : HeLa cells treated by sodium arsenite

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

-
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)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN 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

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1752
ExtractionNumber tomograms: 67 / Number images used: 24873
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more