5U0C

Structure of Zika virus NS5 RNA polymerase domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and function of the Zika virus full-length NS5 protein.

Zhao, B.Yi, G.Du, F.Chuang, Y.C.Vaughan, R.C.Sankaran, B.Kao, C.C.Li, P.

(2017) Nat Commun 8: 14762-14762

  • DOI: 10.1038/ncomms14762
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The recent outbreak of Zika virus (ZIKV) has infected over 1 million people in over 30 countries. ZIKV replicates its RNA genome using virally encoded replication proteins. Nonstructural protein 5 (NS5) contains a methyltransferase for RNA capping an ...

    The recent outbreak of Zika virus (ZIKV) has infected over 1 million people in over 30 countries. ZIKV replicates its RNA genome using virally encoded replication proteins. Nonstructural protein 5 (NS5) contains a methyltransferase for RNA capping and a polymerase for viral RNA synthesis. Here we report the crystal structures of full-length NS5 and its polymerase domain at 3.0 Å resolution. The NS5 structure has striking similarities to the NS5 protein of the related Japanese encephalitis virus. The methyltransferase contains in-line pockets for substrate binding and the active site. Key residues in the polymerase are located in similar positions to those of the initiation complex for the hepatitis C virus polymerase. The polymerase conformation is affected by the methyltransferase, which enables a more efficiently elongation of RNA synthesis in vitro. Overall, our results will contribute to future studies on ZIKV infection and the development of inhibitors of ZIKV replication.


    Organizational Affiliation

    Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA.,Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, 1 Cyclotron Road, Lawrence Berkeley National Lab, Berkeley 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NS5 RNA polymerase domain
A, B, C, D, E, F, G, H
639Zika virusMutation(s): 0 
Find proteins for Q32ZE1 (Zika virus)
Go to UniProtKB:  Q32ZE1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 121.520α = 90.00
b = 188.710β = 91.99
c = 192.539γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
Aimlessdata scaling
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-11-23 
  • Released Date: 2017-03-29 
  • Deposition Author(s): Zhao, B., Du, F.

Revision History 

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-04-12
    Type: Database references