5Z9W

Ebola virus nucleoprotein-RNA complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cryo-EM structure of the Ebola virus nucleoprotein-RNA complex at 3.6 angstrom resolution.

Sugita, Y.Matsunami, H.Kawaoka, Y.Noda, T.Wolf, M.

(2018) Nature 563: 137-140

  • DOI: 10.1038/s41586-018-0630-0

  • PubMed Abstract: 
  • Ebola virus causes haemorrhagic fever with a high fatality rate in humans and non-human primates. It belongs to the family Filoviridae in the order Mononegavirales, which are viruses that contain linear, non-segmented, negative-sense, single-stranded ...

    Ebola virus causes haemorrhagic fever with a high fatality rate in humans and non-human primates. It belongs to the family Filoviridae in the order Mononegavirales, which are viruses that contain linear, non-segmented, negative-sense, single-stranded genomic RNA 1,2 . The enveloped, filamentous virion contains the nucleocapsid, consisting of the helical nucleoprotein-RNA complex, VP24, VP30, VP35 and viral polymerase 1,3 . The nucleoprotein-RNA complex acts as a scaffold for nucleocapsid formation and as a template for RNA replication and transcription by condensing RNA into the virion 4,5 . RNA binding and nucleoprotein oligomerization are synergistic and do not readily occur independently 6 . Although recent cryo-electron tomography studies have revealed the overall architecture of the nucleocapsid core 4,5 , there has been no high-resolution reconstruction of the nucleocapsid. Here we report the structure of a recombinant Ebola virus nucleoprotein-RNA complex expressed in mammalian cells without chemical fixation, at near-atomic resolution using single-particle cryo-electron microscopy. Our structure reveals how the Ebola virus nucleocapsid core encapsidates its viral genome, its sequence-independent coordination with RNA by nucleoprotein, and the dynamic transition between the RNA-free and RNA-bound states. It provides direct structural evidence for the role of the N terminus of nucleoprotein in subunit oligomerization, and for the hydrophobic and electrostatic interactions thatĀ lead to theĀ formation of the helical assembly. The structure is validated as representative of the native biological assembly of the nucleocapsid core by consistent dimensions and symmetry with the full virion 5 . The atomic model provides a detailed mechanistic basis for understanding nucleocapsid assembly and highlights key structural features that may serve as targets for anti-viral drug development.


    Organizational Affiliation

    Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.,Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.,PRESTO, Japan Science and Technology Agency, Saitama, Japan.,Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Laboratory of Advanced Protein Characterization, Research Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University, Osaka, Japan.,Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan. matthias.wolf@oist.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ebolavirus nucleoprotein (residues 19-406)
A
388Zaire ebolavirus (strain Mayinga-76)Mutation(s): 0 
Gene Names: NP
Find proteins for P18272 (Zaire ebolavirus (strain Mayinga-76))
Go to UniProtKB:  P18272
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (6-MER)R6synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
the Ministry of Education, Culture, Science, Sports, and TechnologyJapan26892028
Japan Science and Technology AgencyJapanJPMJPR13L9
Japan Agency for Medical Research and DevelopmentJapan17fk0108128h0001
the Ministry of Education, Culture, Science, Sports, and TechnologyJapan16H06429
the Ministry of Education, Culture, Science, Sports, and TechnologyJapan16K21723
the Ministry of Education, Culture, Science, Sports, and TechnologyJapan16H06434
Japan Society for the Promotion of ScienceJapan--
Daiichi Sankyo Foundation of Life ScienceJapan--
Japan Agency for Medical Research and DevelopmentJapan--

Revision History 

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-11-07
    Type: Data collection, Database references
  • Version 1.2: 2018-11-14
    Type: Data collection, Database references