|Entry||Database: EMDB / ID: EMD-0522|
|Title||Ebola virus nucleoprotein - RNA complex|
|Sample||Ebola virus nucleoprotein bound to RNA:|
Nucleoprotein / nucleic-acidNucleic acid
|Function / homology||Ebola nucleoprotein / Ebola nucleoprotein / viral RNA genome packaging / helical viral capsid / viral nucleocapsid / host cell cytoplasm / Nucleoprotein|
Function and homology information
|Source||Ebola virus - Mayinga, Zaire, 1976 / Zaire ebolavirus (strain Mayinga-76) / Human (human)|
|Method||helical reconstruction / cryo EM / Resolution: 3.1 Å|
|Authors||Kirchdoerfer RN / Ward AB|
|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.
|Validation Report||PDB-ID: 6nut|
SummaryFull reportAbout validation report
|Date||Deposition: Feb 1, 2019 / Header (metadata) release: Feb 27, 2019 / Map release: May 1, 2019 / Update: May 8, 2019|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_0522.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.15 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Ebola virus nucleoprotein bound to RNA
|Entire||Name: Ebola virus nucleoprotein bound to RNA / Number of components: 3|
-Component #1: protein, Ebola virus nucleoprotein bound to RNA
|Protein||Name: Ebola virus nucleoprotein bound to RNA / Recombinant expression: No|
|Mass||Theoretical: 177 MDa|
|Source||Species: Ebola virus - Mayinga, Zaire, 1976|
|Source (engineered)||Expression System: Homo sapiens (human) / Cell of expression system: 293F|
-Component #2: protein, Nucleoprotein
|Protein||Name: Nucleoprotein / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 50.267098 kDa|
|Source||Species: Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76|
|Source (engineered)||Expression System: Homo sapiens (human)|
-Component #3: nucleic-acid, RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
|nucleic acid||Name: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3') / Class: RNA|
Details: The poly-adenosine sequence was modeled to represent the mixed identity of nucleotide sequences bound to nucleoprotein.
Structure: OTHER / Synthetic: No
|Mass||Theoretical: 1.930277 kDa|
|Source||Species: Human (human)|
|Specimen||Specimen state: Filament / Method: cryo EM|
|Helical parameters||Axial symmetry: C1 (asymmetric) / Delta z: 2.84 Å / Delta phi: -14.71 %deg;|
|Sample solution||Specimen conc.: 3.8 mg/mL / pH: 7.4|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Talos Arctica / Image courtesy: FEI Company
|Imaging||Microscope: FEI TALOS ARCTICA|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 49.7 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 47478.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 731|
|Processing||Method: helical reconstruction|
|3D reconstruction||Software: RELION / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF|
|FSC plot (resolution estimation)|
-Atomic model buiding
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