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- EMDB-3873: The structure of Ebola virus nucleocapsid from virions -

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Entry
Database: EMDB / ID: 3873
TitleThe structure of Ebola virus nucleocapsid from virions
SampleEbola virus - Mayinga, Zaire, 1976
SourceEbola virus - Mayinga, Zaire, 1976 / virus
Map dataSubtomogram averaging of Ebola virus nucleocapsid within intact virions
Methodsubtomogram averaging, at 9.1 Å resolution
AuthorsWan W / Kolesnikova L / Clarke M / Koehler A / Noda T / Becker S / Briggs JAG
CitationNature, 2017, 551, 394-397

Nature, 2017, 551, 394-397 Yorodumi Papers
Structure and assembly of the Ebola virus nucleocapsid.
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: Nov 22, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.7
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.7
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_3873.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.78 Å/pix.
= 341.76 Å
192 pix
1.78 Å/pix.
= 341.76 Å
192 pix
1.78 Å/pix.
= 341.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.78 Å
Density
Contour Level:1.7 (by author), 1.7 (movie #1):
Minimum - Maximum-3.650708 - 6.197359
Average (Standard dev.)-0.008506955 (1.0007898)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin000
Limit191191191
Spacing192192192
CellA=B=C: 341.76 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.781.781.78
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z341.760341.760341.760
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-3.6516.197-0.009

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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: 4

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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 / virus
Source (engineered)Expression System: Homo sapiens / human / Cell of expression system: HEK 293T
Shell #1Name of element: Nucleocapsid / Diameter: 280 Å

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Component #2: protein, Ebola virus nucleoprotein

ProteinName: Ebola virus nucleoprotein / Recombinant expression: No
SourceSpecies: Ebola virus - Mayinga, Zaire, 1976 / virus

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Component #3: protein, Ebola virus VP24

ProteinName: Ebola virus VP24 / Recombinant expression: No
SourceSpecies: Ebola virus - Mayinga, Zaire, 1976 / virus

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Component #4: protein, Ebola virus VP35

ProteinName: Ebola virus VP35 / Recombinant expression: No
SourceSpecies: Ebola virus - Mayinga, Zaire, 1976 / virus

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Experimental details

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Sample preparation

Specimen statehelical array
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 - 4500 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: subtomogram averaging / Applied symmetry: C1 (asymmetric)
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. Subtomogram averaging was performed using scripts derived from TOM, AV3, and DYNAMO.
3D reconstructionAlgorithm: BACK PROJECTION / Software: TOM/AV3
CTF correction: CTF amplitude correction was performed during the wedge-weighted subtomogram averaging step.
Resolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Local resolution was estimated using moving window FSC calculations. Resolution varies from 9.1 to 13.8 Angstroms.
Euler angles: Iterative angular search was performed via maximization of a modified constrained cross-correlation function.

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