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- PDB-6ehm: Model of the Ebola virus nucleocapsid subunit from recombinant vi... -

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Database: PDB / ID: 6ehm
TitleModel of the Ebola virus nucleocapsid subunit from recombinant virus-like particles
DescriptorNucleoprotein, Membrane-associated protein VP24
KeywordsVIRUS LIKE PARTICLE / nucleocapsid / virus-like particle
Specimen sourceZaire ebolavirus (strain Mayinga-76) / virus / ZEBOV
MethodElectron microscopy (7.3 Å resolution / Helical array / Subtomogram averaging)
AuthorsWan, W. / Kolesnikova, L. / Clarke, M. / Koehler, A. / Noda, T. / Becker, S. / Briggs, J.A.G.
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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 13, 2017 / Release: Nov 8, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 8, 2017Structure modelrepositoryInitial release
1.1Nov 22, 2017Structure modelDatabase referencescitation_citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
1.2Dec 6, 2017Structure modelDatabase referencescitation_citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
1.3Jan 31, 2018Structure modelAuthor supporting evidence / Data processingem_software / pdbx_audit_support_em_software.name / _em_software.version / _pdbx_audit_support.funding_organization

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Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Membrane-associated protein VP24
D: Membrane-associated protein VP24

Theoretical massNumber of molelcules
Total (without water)223,2774

TypeNameSymmetry operationNumber
identity operation1_5551


#1: Polypeptide(L)Nucleoprotein / Nucleocapsid protein / Protein N / Coordinate model: Cα atoms only

Mass: 83387.500 Da / Num. of mol.: 2
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76) / virus
References: UniProt: P18272

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)Membrane-associated protein VP24 / Coordinate model: Cα atoms only

Mass: 28250.811 Da / Num. of mol.: 2
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76) / virus
References: UniProt: Q05322

Cellular component

Molecular function

Biological process

  • suppression by virus of host intracellular interferon activity (GO: 0046774)
  • viral budding from plasma membrane (GO: 0046761)

Experimental details


EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: SUBTOMOGRAM AVERAGING

Sample preparation

ComponentName: Ebola virus - Mayinga, Zaire, 1976 / Type: VIRUS
Details: Recombinantly expressed virus-like particles produced by expression of nucleoprotein, VP24, VP35, VP40.
Entity ID: 1, 2 / Source: RECOMBINANT
Source (natural)Organism: Ebola virus - Mayinga, Zaire, 1976
Source (recombinant)Cell: HEK 293T / Organism: Homo sapiens
Details of virusEmpty: NO / Enveloped: YES / Virus isolate: STRAIN / Virus type: VIRUS-LIKE PARTICLE
Virus shellName: Nucleocapsid / Diameter: 280 Å
Buffer solutionpH: 7.4
Buffer component
IDConc.UnitsNameFormulaBuffer ID
1100mMsodium chlorideNaCl1
20.1mMethylenediaminetetraacetic acidEDTA1
350mMtrisaminomethane hydrochlorideTris-HCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: C-flat 2/1 3C
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 %

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 / Nominal defocus max: 4500 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 5 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.3 sec. / Electron dose: 3.4 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
EM imaging opticsEnergyfilter name: Gatan Quantum 967 LS / Energyfilter upper: 10 eV / Energyfilter lower: -10 eV
Image scansDimension width: 3708 / Dimension height: 3708 / Movie frames/image: 5 / Used frames/image: 1-5


EM software
IDNameVersionCategoryDetailsImage processing IDImaging IDFitting ID
1Amira4VOLUME SELECTIONplacing spline points1
2TOM ToolboxVOLUME SELECTIONsubtomogram extraction1
5CTFFIND4CTF CORRECTIONdefocus determination1
9UCSF ChimeraMODEL FITTINGRigid body fit1
Image processingDetails: 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.
CTF correctionDetails: CTF amplitude correction was performed during the wedge-weighted subtomogram averaging step.
SymmetryPoint symmetry: C1
3D reconstructionResolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 1 / Algorithm: BACK PROJECTION
Details: Local resolution was estimated using moving window FSC calculations. Resolution varies from 7.3 to 15.2 Angstroms.
Number of class averages: 1 / Symmetry type: POINT
EM volume selectionDetails: Points along the helical axis were manually placed to define a spline. A cylindrical grid as defined at a given radius from the spline; grid spacing was chosen to provide ~4x oversampling.
Number of tomograms: 63 / Number of volumes extracted: 379428 / Reference model: None
Atomic model buildingDetails: Nucleoprotein model from Ebola virus nucleoprotein 1-450 was first rigid body fitted into the inner nucleoprotein densities. Densities were then subtracted, and VP24 pdb was then fit into remaining densities. All models were rigid-body fitted using UCSF Chimera.
Ref protocol: RIGID BODY FIT

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