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- EMDB-3870: Cryo-electron tomogram of Ebola virus nucleoprotein, residues 1-450 -

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Entry
Database: EMDB / ID: 3870
TitleCryo-electron tomogram of Ebola virus nucleoprotein, residues 1-450
SampleEbola virus - Mayinga, Zaire, 1976
SourceEbola virus - Mayinga, Zaire, 1976 / virus
Map dataA 4x binned representative tomogram of recombinant nucleocapsid-like assemblies of Ebola virus nucleoprotein, residues 1-450.
Methodelectron tomography
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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Map

Fileemd_3870.map.gz (map file in CCP4 format, 214833 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
125 pix
7.12 Å/pix.
= 890. Å
927 pix
7.12 Å/pix.
= 6600.24 Å
927 pix
7.12 Å/pix.
= 6600.24 Å

Surface

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Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 7.12 Å
Density
Contour Level:5.5 (by author)
Minimum - Maximum-21 - 26
Average (Standard dev.)2.7605364 (2.3234942)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions927927125
Origin00138
Limit926926262
Spacing927927125
CellA: 6600.2397 Å / B: 6600.2397 Å / C: 890 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z7.127.127.12
M x/y/z927927125
origin x/y/z0.0000.0000.000
length x/y/z6600.2406600.240890.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS00138
NC/NR/NS927927125
D min/max/mean-21.00026.0002.761

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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 / Number of components: 2

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

VirusName: Ebola virus - Mayinga, Zaire, 1976 / Class: VIRUS-LIKE PARTICLE / Empty: No / Enveloped: No / 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, residues 1-450

ProteinName: Ebola virus nucleoprotein, residues 1-450 / Recombinant expression: No
Source (engineered)Expression System: Ebola virus - Mayinga, Zaire, 1976 / virus

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Experimental details

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Sample preparation

Specimen statehelical array
Sample solutionpH: 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: 2.4 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: 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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