5U04

Crystal structure of Zika virus NS5 RNA-dependent RNA polymerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structure of Zika virus NS5 RNA-dependent RNA polymerase.

Godoy, A.S.Lima, G.M.Oliveira, K.I.Torres, N.U.Maluf, F.V.Guido, R.V.Oliva, G.

(2017) Nat Commun 8: 14764-14764

  • DOI: 10.1038/ncomms14764

  • PubMed Abstract: 
  • The current Zika virus (ZIKV) outbreak became a global health threat of complex epidemiology and devastating neurological impacts, therefore requiring urgent efforts towards the development of novel efficacious and safe antiviral drugs. Due to its ce ...

    The current Zika virus (ZIKV) outbreak became a global health threat of complex epidemiology and devastating neurological impacts, therefore requiring urgent efforts towards the development of novel efficacious and safe antiviral drugs. Due to its central role in RNA viral replication, the non-structural protein 5 (NS5) RNA-dependent RNA-polymerase (RdRp) is a prime target for drug discovery. Here we describe the crystal structure of the recombinant ZIKV NS5 RdRp domain at 1.9 Å resolution as a platform for structure-based drug design strategy. The overall structure is similar to other flaviviral homologues. However, the priming loop target site, which is suitable for non-nucleoside polymerase inhibitor design, shows significant differences in comparison with the dengue virus structures, including a tighter pocket and a modified local charge distribution.


    Organizational Affiliation

    Institute of Physics of São Carlos, University of São Paulo, Av. Joao Dagnone, 1100-Jardim Santa Angelina, São Carlos 13563-120, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Zika Virus NS5 RdRp
A
598Zika virus (strain Mr 766)EC: 3.6.1.15, 2.1.1.56, 2.1.1.57, 3.4.21.91, 3.6.4.13, 2.7.7.48
Find proteins for Q32ZE1 (Zika virus (strain Mr 766))
Go to UniProtKB:  Q32ZE1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.179 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.954α = 90.00
b = 78.954β = 90.00
c = 210.022γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
FAPESPBrazil2013/07600-3

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-03-29
    Type: Structure summary
  • Version 1.2: 2017-04-05
    Type: Database references
  • Version 1.3: 2017-04-12
    Type: Database references
  • Version 1.4: 2017-04-26
    Type: Data collection