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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: 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
SampleZika virus-infected Vero E6 cell at 20 hpi
SourceChlorocebus aethiops / mammal / Grivet
Zika virus / virus /
Methodelectron tomography
AuthorsRossignol ED / Bullitt E
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.
Copyright: 2017 John Wiley & Sons Ltd.
DateDeposition: Mar 28, 2017 / Header (metadata) release: Apr 5, 2017 / Map release: Apr 5, 2017 / Last update: Apr 11, 2018

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Structure visualization

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Supplemental images

Downloads & links

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Map

Fileemd_8654.map.gz (map file in CCP4 format, 507511 KB)
Voxel sizeX=Y=Z: 10.86 Å
Density
Contour Level:50 (by emdb)
Minimum - Maximum-128. - 127.
Average (Standard dev.)2.4358144 (23.769362999999998)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions20482048121
Origin0036
Limit20472047156
Spacing20482048121
CellA: 22241.28 Å / B: 22241.28 Å / C: 1314.0599 Å
α=β=γ: 90.0 deg.

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
NX/NY/NZ
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
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.
Number of components: 3

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Component #1: cellular-component, Zika virus-infected Vero E6 cell at 20 hpi

Cellular-componentName: Zika virus-infected Vero E6 cell at 20 hpi
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.
Recombinant expression: No

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Component #2: cellular-component, Vero E6 cell

Cellular-componentName: Vero E6 cell / Recombinant expression: No
SourceSpecies: Chlorocebus aethiops / mammal / Grivet / Strain: Vero E6

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Component #3: virus, Zika virus

VirusName: Zika virus / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Zika virus / virus / / Strain: PRVABC59

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Experimental details

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Sample preparation

Specimen statecell
Sample solutionpH: 7.4
StainingHPF/FS stain of 0.1% UA, 0.1% tannic acid. Post-section stain of 4% UA, 0.2% Reynold's lead citrate
VitrificationCryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 160 kV / Electron dose: 3 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image processing

ProcessingMethod: electron tomography / Number of sections: 222 / Details: Collected using SerialEM
3D reconstructionAlgorithm: EXACT BACK PROJECTION / Software: IMOD

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