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- EMDB-3874: Cryo-electron tomogram of Ebola virus -

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Basic information

Entry
Database: EMDB / ID: 3874
TitleCryo-electron tomogram of Ebola virus
Map dataA 4x binned representative tomogram of intact Ebola virus virions
SampleEbola virus - Mayinga, Zaire, 1976:
virus
SourceEbola virus - Mayinga, Zaire, 1976
Methodelectron tomography / cryo EM
AuthorsWan W / Kolesnikova L / Clarke M / Koehler A / Noda T / Becker S / Briggs JAG
CitationJournal: Nature / Year: 2017
Title: Structure and assembly of the Ebola virus nucleocapsid.
Authors: William Wan / Larissa Kolesnikova / Mairi Clarke / Alexander Koehler / Takeshi Noda / Stephan Becker / John A G Briggs
DateDeposition: Sep 13, 2017 / Header (metadata) release: Nov 22, 2017 / Map release: Nov 22, 2017 / Last update: Apr 18, 2018

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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
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3874.map.gz (map file in CCP4 format, 429665 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
250 pix
7.12 Å/pix.
= 1780. Å
927 pix
7.12 Å/pix.
= 6600.24 Å
927 pix
7.12 Å/pix.
= 6600.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.12 Å
Density
Contour Level:7 (by author)
Minimum - Maximum-40. - 59.
Average (Standard dev.)3.0713525 (3.417756)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions927927250
Origin0042
Limit926926291
Spacing927927250
CellA: 6600.2397 Å / B: 6600.2397 Å / C: 1780.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z7.127.127.12
M x/y/z927927250
origin x/y/z0.0000.0000.000
length x/y/z6600.2406600.2401780.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-128-128-128
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS0042
NC/NR/NS927927250
D min/max/mean-40.00059.0003.071

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Supplemental data

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Sample components

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Entire Ebola virus - Mayinga, Zaire, 1976

EntireName: Ebola virus - Mayinga, Zaire, 1976
Details: Virus was isolated from infected VeroE6 cells. Purified viruses were fixed with paraformaldehyde.
Number of components: 1

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Component #1: virus, Ebola virus - Mayinga, Zaire, 1976

VirusName: Ebola virus - Mayinga, Zaire, 1976 / Class: VIRION
Details: Virus was isolated from infected VeroE6 cells. Purified viruses were fixed with paraformaldehyde.
Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Ebola virus - Mayinga, Zaire, 1976
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK 293T
Shell #1Name of element: Nucleocapsid / Diameter: 280.0 Å

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Experimental details

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Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Sample solutionBuffer solution: Virus was purified into Dulbecco's modified Eagle's medium (DMEM) with 4% paraformaldehyde
pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2.9 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 81000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000.0 - 4500.0 nm / Energy filter: Gatan Quantum 967 LS / Energy window: -10-10 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt Angle: -60 - 60 deg.
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: electron tomography / Tilt angle increment: 3 deg. / Number of sections: 41
Details: Frames were aligned using K2Align software, based off the MotionCorr algorithm. Tomograms were reconstructed with IMOD, using stripwise CTF-correction and weighted back projection.
3D reconstructionAlgorithm: BACK PROJECTION / Software: IMOD

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