|Entry||Database: PDB / ID: 6nut|
|Title||Ebola virus nucleoprotein - RNA complex|
|Keywords||VIRAL PROTEIN/RNA / RNA-binding / nucleoprotein / nucleocapsid / capsid / VIRAL PROTEIN-RNA complex|
|Function / homology||Ebola nucleoprotein / Ebola nucleoprotein / viral RNA genome packaging / helical viral capsid / viral nucleocapsid / host cell cytoplasm / Nucleoprotein|
Function and homology information
|Specimen source||Zaire ebolavirus|
Homo sapiens (human)
|Method||ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.1 Å|
|Authors||Kirchdoerfer, R.N. / Ward, A.B.|
|Funding support||United States , 2件 |
|Citation||Journal: 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.
SummaryFull reportAbout validation report
|Date||Deposition: Feb 1, 2019 / Release: May 1, 2019|
|Structure viewer||Molecule: |
Downloads & links
D: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
A: Nucleoproteinx 50
D: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
|Symmetry||Helical 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 °)|
|#1: Protein/peptide|| |
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|| |
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
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction|
|Component||Name: Ebola virus nucleoprotein bound to RNA / Type: COMPLEX / Entity ID: 1, 2 / Source: RECOMBINANT|
|Molecular weight||Value: 177 kDa/nm / Experimental value: NO|
|Source (natural)||Organism: Ebola virus - Mayinga, Zaire, 1976|
|Source (recombinant)||Organism: Homo sapiens (human) / Cell: 293F|
|Buffer solution||pH: 7.4|
|Specimen||Conc.: 3.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K|
-Electron microscopy imaging
Model: Talos Arctica / Image courtesy: FEI Company
|Microscopy||Model: FEI TALOS ARCTICA|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: 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 holder||Cryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Image recording||Average 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 scans||Width: 3838 / Height: 3710 / Movie frames/image: 65 / Used frames/image: 1-65|
|CTF correction||Type: NONE|
|Helical symmerty||Angular rotation/subunit: -14.71 ° / Axial rise/subunit: 2.84 Å / Axial symmetry: C1|
|Particle selection||Num. of particles selected: 24608|
|3D reconstruction||Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24609 / Num. of class averages: 1 / Symmetry type: HELICAL|
|Atomic model building||Space: REAL|
|Atomic model building|
3D fitting-ID: 1 / Pdb chain-ID: A
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