Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 50.94 kDa 
• Atom Count: 3611 
• Residue Count: 434 
• Unique protein chains: 1

6ADW

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

• DOI: 10.2210/pdb6ADW/pdb

• Classification: HYDROLASE
• Organism(s): Zika virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-02 Released: 2019-03-13 
• Deposition Author(s): Fang, J., Lu, G., Gong, P.
• Funding Organization(s): Natural Science Foundation of Guangdong Province of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.216 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

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

• PubMed: 30672289 
• DOI: 10.1021/acsinfecdis.8b00214
• Structures With Same Primary Citation


• 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. 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.

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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.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Serine protease NS3	A	448	Zika virus	Mutation(s): 0  EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
Find proteins for Q32ZE1 (Zika virus) Go to UniProtKB:  Q32ZE1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	A	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.216 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.532	α = 90
b = 68.534	β = 92.4
c = 56.883	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-08-02 
• Released Date: 2019-03-13 
Deposition Author(s): Fang, J., Lu, G., Gong, P.

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Funding Organization	Location	Grant Number
Natural Science Foundation of Guangdong Province of China	China	2016A030310249

Revision History 

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