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- EMDB-8654: Zika virus-infected Vero E6 cell at 48 hpi: dual-axis tilt series... -

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Entry
Database: EMDB / ID: EMD-8654
TitleZika virus-infected Vero E6 cell at 48 hpi: dual-axis tilt series tomogram from 3 serial sections
Map dataZika virus-infected Vero E6 cell. Example with spherules and convoluted membrane
Sample
  • Cell: Zika virus-infected Vero E6 cell at 20 hpi
    • Cell: Vero E6 cell
    • Virus: Zika virus
Biological speciesChlorocebus aethiops (grivet) / Zika virus
Methodelectron tomography / negative staining
AuthorsRossignol ED / Bullitt E
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102474 United States
NIH/NCRRS10 RR025434 United States
CitationJournal: Cell Microbiol / Year: 2017
Title: Zika virus induced cellular remodelling.
Authors: Evan D Rossignol / Kristen N Peters / John H Connor / Esther Bullitt /
Abstract: Zika virus (ZIKV) has been associated with morbidities such as Guillain-Barré, infant microcephaly, and ocular disease. The spread of this positive-sense, single-stranded RNA virus and its growing ...Zika virus (ZIKV) has been associated with morbidities such as Guillain-Barré, infant microcephaly, and ocular disease. The spread of this positive-sense, single-stranded RNA virus and its growing public health threat underscore gaps in our understanding of basic ZIKV virology. To advance knowledge of the virus replication cycle within mammalian cells, we use serial section 3-dimensional electron tomography to demonstrate the widespread remodelling of intracellular membranes upon infection with ZIKV. We report extensive structural rearrangements of the endoplasmic reticulum and reveal stages of the ZIKV viral replication cycle. Structures associated with RNA genome replication and virus assembly are observed integrated within the endoplasmic reticulum, and we show viruses in transit through the Golgi apparatus for viral maturation, and subsequent cellular egress. This study characterises in detail the 3-dimensional ultrastructural organisation of the ZIKV replication cycle stages. Our results show close adherence of the ZIKV replication cycle to the existing flavivirus replication paradigm.
History
DepositionMar 28, 2017-
Header (metadata) releaseApr 5, 2017-
Map releaseApr 5, 2017-
UpdateJan 29, 2020-
Current statusJan 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Simplified surface model
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8654.png

Downloads & links

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Map

FileDownload / File: emd_8654.map.gz / Format: CCP4 / Size: 484 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationZika virus-infected Vero E6 cell. Example with spherules and convoluted membrane
Voxel sizeX=Y=Z: 10.86 Å
Density
Minimum - Maximum-128 - 127
Average (Standard dev.)2.4358144 (±23.769363)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin0036
Dimensions20482048121
Spacing20482048121
CellA: 22241.28 Å / B: 22241.28 Å / C: 1314.0599 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z10.85999951171910.85999951171910.86
M x/y/z20482048121
origin x/y/z0.0000.0000.000
length x/y/z22241.27922241.2791314.060
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS0036
NC/NR/NS20482048121
D min/max/mean-128.000127.0002.436

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Supplemental data

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Sample components

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Entire : Zika virus-infected Vero E6 cell at 20 hpi

EntireName: Zika virus-infected Vero E6 cell at 20 hpi
Components
  • Cell: Zika virus-infected Vero E6 cell at 20 hpi
    • Cell: Vero E6 cell
    • Virus: Zika virus

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Supramolecule #1: Zika virus-infected Vero E6 cell at 20 hpi

SupramoleculeName: Zika virus-infected Vero E6 cell at 20 hpi / type: cell / ID: 1 / Parent: 0
Details: Cells were infected at a multiplicity of infection of 5 for 20 hours. Cells were fixed, scraped, pelleted, high-pressure frozen/freeze substituted, and embedded in TAAB Epon. Tomogram ...Details: Cells were infected at a multiplicity of infection of 5 for 20 hours. Cells were fixed, scraped, pelleted, high-pressure frozen/freeze substituted, and embedded in TAAB Epon. Tomogram includes 3 joined serial sections, each a dual-axis tomogram.

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Supramolecule #2: Vero E6 cell

SupramoleculeName: Vero E6 cell / type: cell / ID: 2 / Parent: 1
Source (natural)Organism: Chlorocebus aethiops (grivet) / Strain: Vero E6

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Supramolecule #3: Zika virus

SupramoleculeName: Zika virus / type: virus / ID: 3 / Parent: 1 / NCBI-ID: 64320 / Sci species name: Zika virus / Sci species strain: PRVABC59 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Experimental details

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Structure determination

Methodnegative staining
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4
StainingType: NEGATIVE / Material: uranyl accetate, tannic acid, lead citrate
Details: HPF/FS stain of 0.1% UA, 0.1% tannic acid. Post-section stain of 4% UA, 0.2% Reynold's lead citrate
Sugar embeddingMaterial: TAAB epon
High pressure freezingInstrument: OTHER
Details: The value given for _emd_high_pressure_freezing.instrument is Leica. This is not in a list of allowed values set(['LEICA EM PACT2', 'LEICA EM PACT', 'EMS-002 RAPID IMMERSION FREEZER', ...Details: The value given for _emd_high_pressure_freezing.instrument is Leica. This is not in a list of allowed values set(['LEICA EM PACT2', 'LEICA EM PACT', 'EMS-002 RAPID IMMERSION FREEZER', 'OTHER', 'LEICA EM HPM100', 'BAL-TEC HPM 010']) so OTHER is written into the XML file.
SectioningUltramicrotomy - Instrument: Reichert / Ultramicrotomy - Temperature: 273 K / Ultramicrotomy - Final thickness: 180 nm
Fiducial markerManufacturer: Ted Pella / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 160 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsCollected using SerialEM
Final reconstructionAlgorithm: EXACT BACK PROJECTION / Software - Name: IMOD / Number images used: 222

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