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- PDB-6nut: Ebola virus nucleoprotein - RNA complex -

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Basic information

Entry
Database: PDB / ID: 6nut
TitleEbola virus nucleoprotein - RNA complex
Components
  • Nucleoprotein
  • RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
KeywordsVIRAL PROTEIN/RNA / RNA-binding / nucleoprotein / nucleocapsid / capsid / VIRAL PROTEIN-RNA complex
Function / homologyEbola nucleoprotein / Ebola nucleoprotein / viral RNA genome packaging / helical viral capsid / viral nucleocapsid / host cell cytoplasm / Nucleoprotein
Function and homology information
Specimen sourceZaire ebolavirus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKirchdoerfer, R.N. / Ward, A.B.
Funding supportUnited States , 2件
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesAI123498United States
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited States
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2019
Title: Cryo-EM structure of the Ebola virus nucleoprotein-RNA complex.
Authors: Robert N Kirchdoerfer / Erica Ollmann Saphire / Andrew B Ward /
Abstract: Ebola virus is an emerging virus that is capable of causing a deadly disease in humans. Replication, transcription and packaging of the viral genome are carried out by the viral nucleocapsid. The ...Ebola virus is an emerging virus that is capable of causing a deadly disease in humans. Replication, transcription and packaging of the viral genome are carried out by the viral nucleocapsid. The nucleocapsid is a complex of the viral nucleoprotein, RNA and several other viral proteins. The nucleoprotein forms large, RNA-bound, helical filaments and acts as a scaffold for additional viral proteins. The 3.1 Å resolution single-particle cryo-electron microscopy structure of the nucleoprotein-RNA helical filament presented here resembles previous structures determined at lower resolution, while providing improved molecular details of protein-protein and protein-RNA interactions. The higher resolution of the structure presented here will facilitate the design and characterization of novel and specific Ebola virus therapeutics targeting the nucleocapsid.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 1, 2019 / Release: May 1, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 1, 2019Structure modelrepositoryInitial release
1.1May 8, 2019Structure modelData collection / Database referencescitation_citation.page_first / _citation.page_last / _citation.title / _citation.year

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Structure visualization

Movie
  • Biological unit as representative helical assembly
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-0522
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Nucleoprotein
D: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)52,1972
Polymers52,1972
Non-polymers00
Water0
1
A: Nucleoprotein
D: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
x 50


Theoretical massNumber of molelcules
Total (without water)2,609,869100
Polymers2,609,869100
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation50
2


  • Idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 50 / Rise per n subunits: 2.84 Å / Rotation per n subunits: -14.71 °)

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Components

#1: Protein/peptide Nucleoprotein / / Ebola NP / eNP / Nucleocapsid protein / Protein N


Mass: 50267.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76 / Gene: NP / Plasmid: pDisplay / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: P18272
#2: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')


Mass: 1930.277 Da / Num. of mol.: 1
Details: The poly-adenosine sequence was modeled to represent the mixed identity of nucleotide sequences ...The poly-adenosine sequence was modeled to represent the mixed identity of nucleotide sequences bound to nucleoprotein.
Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: 293F

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Ebola virus nucleoprotein bound to RNA / Type: COMPLEX / Entity ID: 1, 2 / Source: RECOMBINANT
Molecular weightValue: 177 kDa/nm / Experimental value: NO
Source (natural)Organism: Ebola virus - Mayinga, Zaire, 1976
Source (recombinant)Organism: Homo sapiens (human) / Cell: 293F
Buffer solutionpH: 7.4
Buffer component

Buffer-ID: 1

IDConc.NameFormula
125 mMTrisC4H11NO3
2150 mMsodium chlorideNaCl
31 mMcalcium chlorideCaCl2
45 mMbeta-mercaptoethanol
SpecimenConc.: 3.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 47478 X / Calibrated defocus min: 600 nm / Calibrated defocus max: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µns
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 13 sec. / Electron dose: 49.7 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 731
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 65 / Used frames/image: 1-65

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Processing

EM software
IDNameVersionCategory
1RELION2.1particle selection
2Leginonimage acquisition
4GctfCTF correction
7Coot0.8.9model fitting
9Rosetta3.1model refinement
10PHENIX1.14rc3-3199model refinement
11RELION3initial Euler assignment
12RELION3final Euler assignment
14RELION33D reconstruction
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -14.71 ° / Axial rise/subunit: 2.84 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 24608
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24609 / Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingSpace: REAL
Atomic model building

3D fitting-ID: 1 / Pdb chain-ID: A

IDPDB-IDPdb chain residue range
14ZTG37-361
25Z9W20-400

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