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- EMDB-13166: Mumps viral factory at a chronic infection stage in a HeLa cell u... -

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Basic information

Entry
Database: EMDB / ID: EMD-13166
TitleMumps viral factory at a chronic infection stage in a HeLa cell under acute arsenite stress
Map dataTomogram of a viral factory in HeLa cells chronically infected by mumps virus after 1 h of 0.5 mM arsenite stress
Sample
  • Cell: Cytoplasmic mumps viral factory at chronic infection stage in a HeLa cell after 1 h of 0.5 mM arsenite stress
KeywordsCryo-ET / cryo-FIB / Helical filament / Nucleocapsid / Protein-RNA complex / Viral factories / Host-virus / VIRUS
Biological speciesMumps virus genotype A
Methodelectron tomography / cryo EM
AuthorsMahamid J / Zhang X
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)760067European Union
CitationJournal: Cell / Year: 2023
Title: Molecular mechanisms of stress-induced reactivation in mumps virus condensates.
Authors: Xiaojie Zhang / Sindhuja Sridharan / Ievgeniia Zagoriy / Christina Eugster Oegema / Cyan Ching / Tim Pflaesterer / Herman K H Fung / Isabelle Becher / Ina Poser / Christoph W Müller / ...Authors: Xiaojie Zhang / Sindhuja Sridharan / Ievgeniia Zagoriy / Christina Eugster Oegema / Cyan Ching / Tim Pflaesterer / Herman K H Fung / Isabelle Becher / Ina Poser / Christoph W Müller / Anthony A Hyman / Mikhail M Savitski / Julia Mahamid /
Abstract: Negative-stranded RNA viruses can establish long-term persistent infection in the form of large intracellular inclusions in the human host and cause chronic diseases. Here, we uncover how cellular ...Negative-stranded RNA viruses can establish long-term persistent infection in the form of large intracellular inclusions in the human host and cause chronic diseases. Here, we uncover how cellular stress disrupts the metastable host-virus equilibrium in persistent infection and induces viral replication in a culture model of mumps virus. Using a combination of cell biology, whole-cell proteomics, and cryo-electron tomography, we show that persistent viral replication factories are dynamic condensates and identify the largely disordered viral phosphoprotein as a driver of their assembly. Upon stress, increased phosphorylation of the phosphoprotein at its interaction interface with the viral polymerase coincides with the formation of a stable replication complex. By obtaining atomic models for the authentic mumps virus nucleocapsid, we elucidate a concomitant conformational change that exposes the viral genome to its replication machinery. These events constitute a stress-mediated switch within viral condensates that provide an environment to support upregulation of viral replication.
History
DepositionJul 3, 2021-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13166.png

Downloads & links

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Map

FileDownload / File: emd_13166.map.gz / Format: CCP4 / Size: 821.3 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationTomogram of a viral factory in HeLa cells chronically infected by mumps virus after 1 h of 0.5 mM arsenite stress
Voxel sizeX=Y=Z: 13.48 Å
Density
Minimum - Maximum-540.0 - 409.0
Average (Standard dev.)2.43104 (±15.420517)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions928928500
Spacing928928500
CellA: 12509.439 Å / B: 12509.439 Å / C: 6740.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_13166_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Tomogram and nucleocapsid tracing of a viral factory...

Fileemd_13166_additional_1.map
AnnotationTomogram and nucleocapsid tracing of a viral factory in HeLa cells chronically infected by mumps virus after 1 h of 0.5 mM arsenite stress
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cytoplasmic mumps viral factory at chronic infection stage in a H...

EntireName: Cytoplasmic mumps viral factory at chronic infection stage in a HeLa cell after 1 h of 0.5 mM arsenite stress
Components
  • Cell: Cytoplasmic mumps viral factory at chronic infection stage in a HeLa cell after 1 h of 0.5 mM arsenite stress

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Supramolecule #1: Cytoplasmic mumps viral factory at chronic infection stage in a H...

SupramoleculeName: Cytoplasmic mumps viral factory at chronic infection stage in a HeLa cell after 1 h of 0.5 mM arsenite stress
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Mumps virus genotype A

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 600 / Focused ion beam - Temperature: 100 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 150
Focused ion beam - Details: Rough milling was done with currents of 1 nA, gradually reduced to lower currents, down to 50 pA for the final polishing step. The value given for _em_focused_ion_beam. ...Focused ion beam - Details: Rough milling was done with currents of 1 nA, gradually reduced to lower currents, down to 50 pA for the final polishing step. The value given for _em_focused_ion_beam.instrument is Aquilos Cryo-FIB. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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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 min: 2.0 µm / Nominal magnification: 42000
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3708 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-11 / Number real images: 58 / Average exposure time: 2.2 sec. / Average electron dose: 2.67 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 58

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