5VI7

Crystal structure of the Zika virus NS3 helicase

• PDB DOI: https://doi.org/10.2210/pdb5VI7/pdb

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


• Deposited: 2017-04-14 Released: 2017-09-06 
• Deposition Author(s): Bukrejewska, M., Derewenda, U., Derewenda, Z.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.207 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Starting Model: experimental

Literature

Crystal structures of the methyltransferase and helicase from the ZIKA 1947 MR766 Uganda strain.

Bukrejewska, M., Derewenda, U., Radwanska, M., Engel, D.A., Derewenda, Z.S.

(2017) Acta Crystallogr D Struct Biol 73: 767-774

• PubMed: 28876240 
• DOI: https://doi.org/10.1107/S2059798317010737
• Primary Citation of Related Structures:  
  5VI7, 5VIM


• PubMed Abstract: 
  

  Two nonstructural proteins encoded by Zika virus strain MR766 RNA, a methyltransferase and a helicase, were crystallized and their structures were solved and refined at 2.10 and 2.01 Å resolution, respectively. The NS5 methyltransferase contains a bound S-adenosyl-L-methionine (SAM) co-substrate. The NS3 helicase is in the apo form. Comparison with published crystal structures of the helicase in the apo, nucleotide-bound and single-stranded RNA (ssRNA)-bound states suggests that binding of ssRNA to the helicase may occur through conformational selection rather than induced fit.

---

Organizational Affiliation: 

Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908-0736, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 50.37 kDa 
• Atom Count: 3,804 
• Modelled Residue Count: 435 
• Deposited Residue Count: 443 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
helicase	A	443	Zika virus	Mutation(s): 0  EC: 3.6.4.13
UniProt
Find proteins for Q32ZE1 (Zika virus) Explore Q32ZE1  Go to UniProtKB:  Q32ZE1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.207 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.606	α = 90
b = 79.468	β = 90
c = 119.769	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-06 
Deposition Author(s): Bukrejewska, M., Derewenda, U., Derewenda, Z.S.

Revision History  

• Version 1.0: 2017-09-06
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection, Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description