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- EMDB-3869: The structure of Ebola virus nucleoprotein (residues 1-450) in nu... -

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Basic information

Database: EMDB / ID: 3869
TitleThe structure of Ebola virus nucleoprotein (residues 1-450) in nucleocapsid-like assemblies
Map dataSubtomogram averaging of recombinantly expressed Ebola Nucleoprotein (NP), residues 1-450
SampleEbola virus - Mayinga, Zaire, 1976:
virus / Nucleoprotein
Function / homologyEbola nucleoprotein / Ebola nucleoprotein / viral RNA genome packaging / helical viral capsid / viral nucleocapsid / host cell cytoplasm / RNA binding / Nucleoprotein
Function and homology information
SourceEbola virus - Mayinga, Zaire, 1976
Methodsubtomogram averaging / cryo EM / 6.6 Å resolution
AuthorsWan W / Kolesnikova L
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
Validation ReportPDB-ID: 6ehl

SummaryFull reportAbout validation report
DateDeposition: Sep 13, 2017 / Header (metadata) release: Nov 8, 2017 / Map release: Nov 8, 2017 / Last update: Jan 31, 2018

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6ehl
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6ehl
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_3869.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

Image control

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.78 Å
Contour Level:2.5 (by author), 2.5 (movie #1):
Minimum - Maximum-3.2473512 - 8.931272
Average (Standard dev.)-0.022757614 (1.0010257)


Space Group Number1
Map Geometry
Axis orderXYZ
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
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-3.2478.931-0.023

Supplemental data

Sample components

Entire Ebola virus - Mayinga, Zaire, 1976

EntireName: Ebola virus - Mayinga, Zaire, 1976 / Number of components: 2

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

Component #2: protein, Nucleoprotein

ProteinName: Nucleoprotein / Recombinant expression: No
MassTheoretical: 83.3875 kDa
Source (engineered)Expression System: Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76

Experimental details

Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 %

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)

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: AV3
CTF correction: CTF amplitude correction was performed during the wedge-weighted subtomogram averaging step.
Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Local resolution was estimated using moving window FSC calculations.
Euler angles: Iterative angular search was performed via maximization of a modified constrained cross-correlation function.

Atomic model buiding

Output model

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