|Entry||Database: EMDB / ID: 3869|
|Title||The structure of Ebola virus nucleoprotein (residues 1-450) in nucleocapsid-like assemblies|
|Map data||Subtomogram averaging of recombinantly expressed Ebola Nucleoprotein (NP), residues 1-450|
|Sample||Ebola virus - Mayinga, Zaire, 1976:|
virus / Nucleoprotein
|Function / homology||Ebola nucleoprotein / Ebola nucleoprotein / viral RNA genome packaging / helical viral capsid / viral nucleocapsid / host cell cytoplasm / RNA binding / Nucleoprotein|
Function and homology information
|Source||Ebola virus - Mayinga, Zaire, 1976|
|Method||subtomogram averaging / cryo EM / 6.6 Å resolution|
|Authors||Wan W / Kolesnikova L|
|Citation||Journal: 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 Report||PDB-ID: 6ehl|
SummaryFull reportAbout validation report
|Date||Deposition: Sep 13, 2017 / Header (metadata) release: Nov 8, 2017 / Map release: Nov 8, 2017 / Last update: Jan 31, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_3869.map.gz (map file in CCP4 format, 28312 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.78 Å|
CCP4 map header:
-Entire Ebola virus - Mayinga, Zaire, 1976
|Entire||Name: Ebola virus - Mayinga, Zaire, 1976 / Number of components: 2|
-Component #1: virus, Ebola virus - Mayinga, Zaire, 1976
|Virus||Name: Ebola virus - Mayinga, Zaire, 1976 / Class: VIRUS-LIKE PARTICLE / Empty: No / Enveloped: No / Isolate: STRAIN|
|Species||Species: Ebola virus - Mayinga, Zaire, 1976|
|Source (engineered)||Expression System: Homo sapiens (human) / Cell of expression system: HEK 293T|
|Shell #1||Name of element: Nucleocapsid / Diameter: 280 Å|
-Component #2: protein, Nucleoprotein
|Protein||Name: Nucleoprotein / Recombinant expression: No|
|Mass||Theoretical: 83.3875 kDa|
|Source (engineered)||Expression System: Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76|
|Specimen||Specimen state: helical array / Method: cryo EM|
|Sample solution||pH: 7.4|
|Vitrification||Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2.4 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 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 Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt Angle: -60 - 60 deg.|
|Camera||Detector: GATAN K2 QUANTUM (4k x 4k)|
|Processing||Method: 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 reconstruction||Algorithm: 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.
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