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- PDB-5z9w: Ebola virus nucleoprotein-RNA complex -

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Basic information

Entry
Database: PDB / ID: 5z9w
TitleEbola virus nucleoprotein-RNA complex
Components
  • Ebolavirus nucleoprotein (residues 19-406)
  • RNA (6-MER)
KeywordsVIRAL PROTEIN / ebolavirus / RNA / nucleoprotein / nucleocapsid / helical
Specimen sourceHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 3.6 Å resolution
AuthorsSugita, Y. / Matsunami, H. / Kawaoka, Y. / Noda, T. / Wolf, M.
CitationJournal: Nature / Year: 2018
Title: Cryo-EM structure of the Ebola virus nucleoprotein-RNA complex at 3.6 Å resolution.
Authors: Yukihiko Sugita / Hideyuki Matsunami / Yoshihiro Kawaoka / Takeshi Noda / Matthias Wolf
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 5, 2018 / Release: Oct 24, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 24, 2018Structure modelrepositoryInitial release
1.1Nov 7, 2018Structure modelData collection / Database referencescitation_citation.pdbx_database_id_PubMed
1.2Nov 14, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

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  • Biological unit as representative helical assembly
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Ebolavirus nucleoprotein (residues 19-406)
R: RNA (6-MER)


Theoretical massNumber of molelcules
Total (without water)45,2882
Polyers45,2882
Non-polymers00
Water0
1
A: Ebolavirus nucleoprotein (residues 19-406)
R: RNA (6-MER)
x 51


Theoretical massNumber of molelcules
Total (without water)2,309,694102
Polyers2,309,694102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
transform to helical frame1
helical symmetry operation50
Helical symmetryNumber of operations: 51

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Components

#1: Protein/peptide Ebolavirus nucleoprotein (residues 19-406)


Mass: 43496.086 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Cell (production host): epithelial / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / Tissue (production host): embryonic kidney
#2: RNA chain RNA (6-MER)


Mass: 1792.037 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Ebolavirus nucleoprotein RNA complex (biological assembly)
Type: COMPLEX / Entity ID: 1, 2 / Source: RECOMBINANT
Molecular weightValue: 0.166 MDa / Experimental value: NO
Source (natural)Organism: Ebola virus - Mayinga, Zaire, 1976
Source (recombinant)Cell: HEK293T / Organism: Homo sapiens (human)
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer ID
110 mMTris-HClC4H12ClNO31
2150 mMsodium chlorideNaCl1
31 mMEDTAC10H12O8CaN2Na2x2H2O1
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Gatan Solarus / Grid material: COPPER / Grid mesh size: 400 / Grid type: C-flat-1.2/1.3 4C
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 kelvins / Details: 3 second blot, 2.5uL

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Details: nanoprobe, parallel beam illumination
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 / Calibrated magnification: 47619 / Nominal defocus max: 4000 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 4000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 kelvins / Temperature (min): 77 kelvins / Residual tilt: 0.1 mradians
Image recordingAverage exposure time: 15 sec. / Electron dose: 105 e/Å2
Details: frame alignment and dose weighting using motioncor2
Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 2467
EM imaging opticsEnergyfilter name: GIF Quantum LS
Image scansSampling size: 5 microns / Width: 7676 / Height: 7420 / Movie frames/image: 75 / Used frames/image: 1-75

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EMAN22.1particle selectione2helixboxer.py
2Leginon3.2image acquisition
4CTFFIND4.1CTF correction
7Coot0.8.7model fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIX1.13rc2-2981model refinementphenix.real_space_refine
Image processingDetails: frame alignment and integration with motioncor2 incl. dose weighting and 2x Fourier cropping
CTF correctionDetails: deconvolution in RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -14.73 deg. / Axial rise/subunit: 3.01 Å / Axial symmetry: D1
Particle selectionNumber of particles selected: 232490
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 117552 / Algorithm: FOURIER SPACE / Number of class averages: 3 / Symmetry type: POINT
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: REAL
Least-squares processHighest resolution: 3.9 Å

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