6ADW

Crystal structure of the Zika virus NS3 helicase (apo form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystallographic Snapshots of the Zika Virus NS3 Helicase Help Visualize the Reactant Water Replenishment.

Fang, J.Jing, X.Lu, G.Xu, Y.Gong, P.

(2019) ACS Infect Dis 5: 177-183

  • DOI: 10.1021/acsinfecdis.8b00214
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Zika virus (ZIKV), a positive-strand RNA virus belonging to the Flavivirus genus, has become an urgent public health concern since recent outbreaks worldwide. Its genome replication is facilitated by the viral NS3 protein bearing helicase function. T ...

    Zika virus (ZIKV), a positive-strand RNA virus belonging to the Flavivirus genus, has become an urgent public health concern since recent outbreaks worldwide. Its genome replication is facilitated by the viral NS3 protein bearing helicase function. The NS3 helicase uses energy derived from adenosine triphosphate (ATP) hydrolysis to unwind RNA duplexed regions. Structural studies of the flavivirus NS3 helicases have suggested a conserved mechanism of ATP hydrolysis. However, the process of the reactant water replenishment, a key part of the hydrolysis cycle, remains elusive. Here, we report two high-resolution crystal structures of ZIKV NS3 helicase in complex with adenosine diphosphate (ADP) and Mn 2+ , one with the reactant water already loaded as previously observed and the other with the water molecule still in a loading state. These data suggest that the reactant water replenishment can occur between the release of phosphate and the release of ADP and improves the structural basis of the NS3 ATP hydrolysis cycle.


    Organizational Affiliation

    Key Laboratory of Special Pathogens and Biosafety , Wuhan Institute of Virology, Chinese Academy of Sciences , No. 44 Xiao Hong Shan , Wuhan , Hubei 430071 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China.,The Joint Center of Translational Precision Medicine, Wuhan Institute of Virology , Chinese Academy of Sciences , No. 44 Xiao Hong Shan , Wuhan , Hubei , 430071 , China.,The Joint Center of Translational Precision Medicine, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, No. 318 Renminzhonglu , Guangzhou , Guangdong 510623 , China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine protease NS3
A
448Zika virusMutation(s): 0 
Find proteins for Q32ZE1 (Zika virus)
Go to UniProtKB:  Q32ZE1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 53.532α = 90.00
b = 68.534β = 92.40
c = 56.883γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXrefinement
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Science Foundation of Guangdong Province of ChinaChina2016A030310249

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release