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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
SampleZika virus-infected Vero E6 cell at 20 hpi
SourceChlorocebus aethiops / mammal / ミドリザル
Zika virus / virus / ジカウイルス
Map dataZika virus-infected Vero E6 cell. Example with spherules and convoluted membrane
Methodelectron tomography
AuthorsRossignol ED / Bullitt E
CitationCell. Microbiol., 2017

Cell. Microbiol., 2017 StrPapers
Zika virus induced cellular remodelling.
Evan D Rossignol / Kristen N Peters / John H Connor / Esther Bullitt

DateDeposition: Mar 28, 2017 / Header (metadata) release: Apr 5, 2017 / Map release: Apr 5, 2017 / Last update: Mar 28, 2017

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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 (23.769363)
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
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
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 / ミドリザル / Strain: Vero E6

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Component #3: virus, Zika virus

VirusName: Zika virus
SpeciesSpecies: Zika virus / virus / ジカウイルス / 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: 30 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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