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- EMDB-15391: Subtomogram average of RNA-loaded poliovirus -

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Basic information

Entry
Database: EMDB / ID: EMD-15391
TitleSubtomogram average of RNA-loaded poliovirus
Map dataSubtomogram average of RNA-loaded poliovirus
Sample
  • Virus: Human poliovirus 1 Mahoney
Keywordspoliovirus / cellular tomography / in situ / VIRUS
Biological speciesHuman poliovirus 1 Mahoney
Methodsubtomogram averaging / cryo EM / Resolution: 28.0 Å
AuthorsDahmane S / Carlson LA
Funding support France, European Union, Sweden, 3 items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)CDA00047/2017-C France
European Commission795892European Union
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nat Commun / Year: 2022
Title: Membrane-assisted assembly and selective secretory autophagy of enteroviruses.
Authors: Selma Dahmane / Adeline Kerviel / Dustin R Morado / Kasturika Shankar / Björn Ahlman / Michael Lazarou / Nihal Altan-Bonnet / Lars-Anders Carlson /
Abstract: Enteroviruses are non-enveloped positive-sense RNA viruses that cause diverse diseases in humans. Their rapid multiplication depends on remodeling of cytoplasmic membranes for viral genome ...Enteroviruses are non-enveloped positive-sense RNA viruses that cause diverse diseases in humans. Their rapid multiplication depends on remodeling of cytoplasmic membranes for viral genome replication. It is unknown how virions assemble around these newly synthesized genomes and how they are then loaded into autophagic membranes for release through secretory autophagy. Here, we use cryo-electron tomography of infected cells to show that poliovirus assembles directly on replication membranes. Pharmacological untethering of capsids from membranes abrogates RNA encapsidation. Our data directly visualize a membrane-bound half-capsid as a prominent virion assembly intermediate. Assembly progression past this intermediate depends on the class III phosphatidylinositol 3-kinase VPS34, a key host-cell autophagy factor. On the other hand, the canonical autophagy initiator ULK1 is shown to restrict virion production since its inhibition leads to increased accumulation of virions in vast intracellular arrays, followed by an increased vesicular release at later time points. Finally, we identify multiple layers of selectivity in virus-induced autophagy, with a strong selection for RNA-loaded virions over empty capsids and the segregation of virions from other types of autophagosome contents. These findings provide an integrated structural framework for multiple stages of the poliovirus life cycle.
History
DepositionJul 14, 2022-
Header (metadata) releaseOct 19, 2022-
Map releaseOct 19, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15391.png

Downloads & links

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Map

FileDownload / File: emd_15391.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of RNA-loaded poliovirus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.29 Å/pix.
x 140 pix.
= 600.6 Å		4.29 Å/pix.
x 140 pix.
= 600.6 Å		4.29 Å/pix.
x 140 pix.
= 600.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.29 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-1.3545407 - 1.883482
Average (Standard dev.)0.007866917 (±0.29086158)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-70-70-70
Dimensions140140140
Spacing140140140
CellA=B=C: 600.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15391_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_15391_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_15391_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human poliovirus 1 Mahoney

EntireName: Human poliovirus 1 Mahoney
Components
  • Virus: Human poliovirus 1 Mahoney

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Supramolecule #1: Human poliovirus 1 Mahoney

SupramoleculeName: Human poliovirus 1 Mahoney / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 12081 / Sci species name: Human poliovirus 1 Mahoney / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 3.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 3.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 13 / Number images used: 556
Final 3D classificationNumber classes: 1 / Avg.num./class: 1
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: Dynamo
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 357

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