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- EMDB-3875: The structure of Marburg virus nucleocapsid from virions -

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Basic information

Entry
Database: EMDB / ID: 3875
TitleThe structure of Marburg virus nucleocapsid from virions
Map dataSubtomogram averaging of Marburg virus nucleocapsid within intact virions
SampleLake Victoria marburgvirus - Popp:
virus / Marburg nucleoprotein / Marburg VP24 / Marburg VP35
SourceLake Victoria marburgvirus - Popp / Marburg virus - Musoke, Kenya, 1980 / Marburg virus - Angola
Methodsubtomogram averaging / cryo EM / 9.1 Å resolution
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
  • Surface view with section colored by density value
  • Surface level: 1.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3875.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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.

Voxel sizeX=Y=Z: 1.78 Å
Density
Contour Level:1.3 (by author), 1.3 (movie #1):
Minimum - Maximum-5.4403253 - 8.994699000000001
Average (Standard dev.)-0.024126286 (0.9858234)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin000
Limit191191191
Spacing192192192
CellA=B=C: 341.76 Å
α=β=γ: 90.0 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-128-128-128
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-5.4408.995-0.024

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Supplemental data

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Sample components

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Entire Lake Victoria marburgvirus - Popp

EntireName: Lake Victoria marburgvirus - Popp
Details: Virus was isolated from infected Huh-7 cells. Purified viruses were fixed with paraformaldehyde.
Number of components: 4

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Component #1: virus, Lake Victoria marburgvirus - Popp

VirusName: Lake Victoria marburgvirus - Popp / Class: VIRION
Details: Virus was isolated from infected Huh-7 cells. Purified viruses were fixed with paraformaldehyde.
Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Lake Victoria marburgvirus - Popp
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK 293T
Shell #1Name of element: Nucleocapsid / Diameter: 310.0 Å

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Component #2: protein, Marburg nucleoprotein

ProteinName: Marburg nucleoprotein / Recombinant expression: No
SourceSpecies: Marburg virus - Musoke, Kenya, 1980

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Component #3: protein, Marburg VP24

ProteinName: Marburg VP24 / Recombinant expression: No
SourceSpecies: Marburg virus - Musoke, Kenya, 1980

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Component #4: protein, Marburg VP35

ProteinName: Marburg VP35 / Recombinant expression: No
SourceSpecies: Marburg virus - Angola

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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: 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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