5JRZ | pdb_00005jrz

Structure of the NS3 helicase from the French Polynesia strain of the Zika virus

• PDB DOI: https://doi.org/10.2210/pdb5JRZ/pdb

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


• Deposited: 2016-05-06 Released: 2016-07-06 
• Deposition Author(s): Jain, R., Coloma, J., Aggarwal, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Structure of the NS3 helicase from Zika virus.

Jain, R., Coloma, J., Garcia-Sastre, A., Aggarwal, A.K.

(2016) Nat Struct Mol Biol 23: 752-754

• PubMed: 27399257 
• DOI: https://doi.org/10.1038/nsmb.3258
• Primary Citation of Related Structures:  
  5JRZ


• PubMed Abstract: 
  

  Zika virus has emerged as a pathogen of major health concern. Here, we present a high-resolution (1.62-Å) crystal structure of the RNA helicase from the French Polynesia strain. The structure is similar to that of the RNA helicase from Dengue virus, with variability in the conformations of loops typically involved in binding ATP and RNA. We identify druggable 'hotspots' that are well suited for in silico and/or fragment-based high-throughput drug discovery.

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Organizational Affiliation: 

Department of Structural &Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York, 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: 51.08 kDa 
• Atom Count: 4,038 
• Modelled Residue Count: 443 
• Deposited Residue Count: 449 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Helicase	A	449	Zika virus	Mutation(s): 0
UniProt
Find proteins for Q32ZE1 (Zika virus) Explore Q32ZE1  Go to UniProtKB:  Q32ZE1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
POP	H [auth A]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
ACT	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.304	α = 90
b = 71.864	β = 94.6
c = 59.281	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
Auto-Rickshaw	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-06 
Deposition Author(s): Jain, R., Coloma, J., Aggarwal, A.K.

Revision History  

• Version 1.0: 2016-07-06
  Type: Initial release
  
• Version 1.1: 2016-07-13
  Changes: Source and taxonomy, Structure summary
• Version 1.2: 2016-08-17
  Changes: Database references
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description