|Entry||Database: EMDB / ID: 7343|
|Title||Ebola nucleoprotein nucleocapsid-like assembly and the asymmetric unit|
|Map data||Ebola nucleoprotein nucleocapsid-like assembly|
|Sample||eNP nucleocapsid-like assembly:|
|Function / homology||Ebola nucleoprotein / Ebola nucleoprotein / viral RNA genome packaging / helical viral capsid / host cell cytoplasm / viral nucleocapsid / RNA binding / Nucleoprotein / Nucleoprotein|
Function and homology information
|Method||helical reconstruction / cryo EM / 5.8 Å resolution|
|Authors||Su Z / Wu C|
Journal: Cell / Year: 2018
Title: Electron Cryo-microscopy Structure of Ebola Virus Nucleoprotein Reveals a Mechanism for Nucleocapsid-like Assembly.
Authors: Zhaoming Su / Chao Wu / Liuqing Shi / Priya Luthra / Grigore D Pintilie / Britney Johnson / Justin R Porter / Peng Ge / Muyuan Chen / Gai Liu / Thomas E Frederick / Jennifer M Binning / Gregory R Bowman / Z Hong Zhou / Christopher F Basler / Michael L Gross / Daisy W Leung / Wah Chiu / Gaya K Amarasinghe
Abstract: Ebola virus nucleoprotein (eNP) assembles into higher-ordered structures that form the viral nucleocapsid (NC) and serve as the scaffold for viral RNA synthesis. However, molecular insights into the ...Ebola virus nucleoprotein (eNP) assembles into higher-ordered structures that form the viral nucleocapsid (NC) and serve as the scaffold for viral RNA synthesis. However, molecular insights into the NC assembly process are lacking. Using a hybrid approach, we characterized the NC-like assembly of eNP, identified novel regulatory elements, and described how these elements impact function. We generated a three-dimensional structure of the eNP NC-like assembly at 5.8 Å using electron cryo-microscopy and identified a new regulatory role for eNP helices α22-α23. Biochemical, biophysical, and mutational analyses revealed that inter-eNP contacts within α22-α23 are critical for viral NC assembly and regulate viral RNA synthesis. These observations suggest that the N terminus and α22-α23 of eNP function as context-dependent regulatory modules (CDRMs). Our current study provides a framework for a structural mechanism for NC-like assembly and a new therapeutic target.
#1: Journal: Cell Rep / Year: 2015
Title: An Intrinsically Disordered Peptide from Ebola Virus VP35 Controls Viral RNA Synthesis by Modulating Nucleoprotein-RNA Interactions.
Authors: Daisy W Leung / Dominika Borek / Priya Luthra / Jennifer M Binning / Manu Anantpadma / Gai Liu / Ian B Harvey / Zhaoming Su / Ariel Endlich-Frazier / Juanli Pan / Reed S Shabman / Wah Chiu / Robert A Davey / Zbyszek Otwinowski / Christopher F Basler / Gaya K Amarasinghe
Abstract: During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In ...During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented from indiscriminately binding to noncognate RNAs. Here, we investigate the molecular bases for these critical processes. We identify an intrinsically disordered peptide derived from EBOV VP35 (NPBP, residues 20-48) that binds NP with high affinity and specificity, inhibits NP oligomerization, and releases RNA from NP-RNA complexes in vitro. The structure of the NPBP/ΔNPNTD complex, solved to 3.7 Å resolution, reveals how NPBP peptide occludes a large surface area that is important for NP-NP and NP-RNA interactions and for viral RNA synthesis. Together, our results identify a highly conserved viral interface that is important for EBOV replication and can be targeted for therapeutic development.
|Validation Report||PDB-ID: 6c54|
SummaryFull reportAbout validation report
|Date||Deposition: Jan 13, 2018 / Header (metadata) release: Feb 14, 2018 / Map release: Mar 7, 2018 / Last update: Mar 7, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_7343.map.gz (map file in CCP4 format, 73600 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 2.4 Å|
CCP4 map header:
-Entire eNP nucleocapsid-like assembly
|Entire||Name: eNP nucleocapsid-like assembly / Number of components: 2|
-Component #1: protein, eNP nucleocapsid-like assembly
|Protein||Name: eNP nucleocapsid-like assembly / Recombinant expression: No|
|Source||Species: Zaire ebolavirus|
|Source (engineered)||Expression System: Escherichia coli (E. coli)|
-Component #2: protein, Nucleoprotein
|Protein||Name: Nucleoprotein / Recombinant expression: No|
|Mass||Theoretical: 48.14259 kDa|
|Source (engineered)||Expression System: Zaire ebolavirus|
|Specimen||Specimen state: filament / Method: cryo EM|
|Helical parameters||Axial symmetry: C1 (asymmetric) / Delta z: 2.65 Å / Delta phi: -8.53 deg.|
|Sample solution||Specimen conc.: 5 mg/ml|
Buffer solution: 150 mM NaCl, 3 mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 100 %|
-Electron microscopy imaging
|Imaging||Microscope: JEOL 3200FSC|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 24 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 30000 X (nominal) / Cs: 4.7 mm / Imaging mode: BRIGHT FIELD / Energy filter: In-column Omega Filter / Energy window: 30-30 eV|
|Specimen Holder||Model: JEOL 3200FSC CRYOHOLDER / Temperature: K ( 86 - 86 K)|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Image acquisition||Number of digital images: 1266|
|Processing||Method: helical reconstruction|
|3D reconstruction||Software: RELION / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
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