6LNU

Cryo-EM structure of immature Zika virus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Capsid protein structure in Zika virus reveals the flavivirus assembly process.

Tan, T.Y.Fibriansah, G.Kostyuchenko, V.A.Ng, T.S.Lim, X.X.Zhang, S.Lim, X.N.Wang, J.Shi, J.Morais, M.C.Corti, D.Lok, S.M.

(2020) Nat Commun 11: 895-895

  • DOI: 10.1038/s41467-020-14647-9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Structures of flavivirus (dengue virus and Zika virus) particles are known to near-atomic resolution and show detailed structure and arrangement of their surface proteins (E and prM in immature virus or M in mature virus). By contrast, the arrangemen ...

    Structures of flavivirus (dengue virus and Zika virus) particles are known to near-atomic resolution and show detailed structure and arrangement of their surface proteins (E and prM in immature virus or M in mature virus). By contrast, the arrangement of the capsid proteins:RNA complex, which forms the core of the particle, is poorly understood, likely due to inherent dynamics. Here, we stabilize immature Zika virus via an antibody that binds across the E and prM proteins, resulting in a subnanometer resolution structure of capsid proteins within the virus particle. Fitting of the capsid protein into densities shows the presence of a helix previously thought to be removed via proteolysis. This structure illuminates capsid protein quaternary organization, including its orientation relative to the lipid membrane and the genomic RNA, and its interactions with the transmembrane regions of the surface proteins. Results show the capsid protein plays a central role in the flavivirus assembly process.


    Organizational Affiliation

    Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.,CryoEM Unit, Department of Biological Sciences, National University of Singapore, Singapore, 117557, Singapore.,Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, 169857, Singapore.,Humabs BioMed SA, a subsidiary of Vir Biotechnology, Inc., CH-6500, Bellinzona, Switzerland.,Centre for BioImaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, 117557, Singapore.,Centre for BioImaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, 117557, Singapore. sheemei.lok@duke-nus.edu.sg.,Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, 169857, Singapore. sheemei.lok@duke-nus.edu.sg.,Department of Biochemistry and Molecular Biology, Sealy Center for Structural and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, 77555-0647, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Genome polyprotein
A, B, C
504Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)Mutation(s): 0 
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013))
Go to UniProtKB:  A0A024B7W1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Genome polyprotein
D, E, F
163Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)Mutation(s): 0 
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013))
Go to UniProtKB:  A0A024B7W1
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (MoE, Singapore)SingaporeMOE2012-T3-1-008
National Research Foundation (NRF, Singapore)SingaporeNRF-NRFI2016-01
National Research Foundation (NRF, Singapore)SingaporeNRF2015NRF-CRP001-063

Revision History 

  • Version 1.0: 2020-02-26
    Type: Initial release