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- EMDB-48641: Free 40S consensus structure, from VacV infected cells -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-48641
TitleFree 40S consensus structure, from VacV infected cells
Map data
Sample
  • Complex: Free 40S, from VacV infected cells
KeywordsNone / RIBOSOME
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsPark C / Ferrell AJ / Shen PS / Walsh D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI127456 United States
CitationJournal: Nat Microbiol / Year: 2025
Title: Distinct non-canonical translation initiation modes arise for specific host and viral mRNAs during poxvirus-induced shutoff.
Authors: Chorong Park / Aaron J Ferrell / Nathan Meade / Peter S Shen / Derek Walsh /
Abstract: Many viruses potently inhibit host protein synthesis, termed host shutoff, while employing strategies to sustain their own translation. How and why certain host mRNAs continue to be translated at ...Many viruses potently inhibit host protein synthesis, termed host shutoff, while employing strategies to sustain their own translation. How and why certain host mRNAs continue to be translated at later infection stages remains unclear. Here, using RNAseq and polysome profiling, we show that during shutoff by vaccinia virus (VacV), several host mRNAs increase in polysome occupancy but only a few, primarily JUN that encodes the Jun transcription factor, result in increased protein abundance across multiple cell lines. While dispensable for Jun production, translation of viral mRNAs depended on the small ribosomal protein, Receptor for Activated C Kinase 1 (RACK1) and the eukaryotic Initiation Factor, eIF3. These differential eIF3 dependencies are associated with structurally distinct 5' untranslated regions in viral versus JUN mRNAs. Cryo-electron microscopy structures of 40S ribosomes from mock-infected or VacV-infected cells showed that when bound to eIF3, the rotational range of the RACK1-containing 40S head domain broadens during infection. Our data reveal how eIF3-bound 40S ribosomes are remodelled late in infection and the distinct strategies of translation initiation that arise during shutoff to produce host and viral proteins required for poxvirus spread.
History
DepositionJan 14, 2025-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48641.png

Downloads & links

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Map

FileDownload / File: emd_48641.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 420 pix.
= 444.36 Å		1.06 Å/pix.
x 420 pix.
= 444.36 Å		1.06 Å/pix.
x 420 pix.
= 444.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.47237504 - 1.1996546
Average (Standard dev.)0.0012772828 (±0.036060363)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 444.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_48641_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48641_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Free 40S, from VacV infected cells

EntireName: Free 40S, from VacV infected cells
Components
  • Complex: Free 40S, from VacV infected cells

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Supramolecule #1: Free 40S, from VacV infected cells

SupramoleculeName: Free 40S, from VacV infected cells / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2 MDa

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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: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 156323
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)

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