6RWZ

Structure of Zika virus NS3 helicase in complex with ADP-BeF3

• PDB DOI: https://doi.org/10.2210/pdb6RWZ/pdb

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


• Deposited: 2019-06-07 Released: 2020-07-15 
• Deposition Author(s): Ge, M., Molt Jr., R.W., Jenkins, H.T., Blackburn, G.M., Jin, Y., Antson, A.A.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.206 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Starting Model: experimental

Literature

Octahedral Trifluoromagnesate, an Anomalous Metal Fluoride Species, Stabilizes the Transition State in a Biological Motor.

Ge, M., Molt Jr., R.W., Jenkins, H.T., Blackburn, G.M., Jin, Y., Antson, A.A.

(2021) ACS Catal 11: 2769-2773

• PubMed: 33717640 
• DOI: https://doi.org/10.1021/acscatal.0c04500
• Primary Citation of Related Structures:  
  6RWZ, 6S0J


• PubMed Abstract: 
  

  Isoelectronic metal fluoride transition state analogue (TSA) complexes, MgF ₃ ^- and AlF ₄ ^- , have proven to be immensely useful in understanding mechanisms of biological motors utilizing phosphoryl transfer. Here we report a previously unobserved octahedral TSA complex, MgF ₃ (H ₂ O) ^- , in a 1.5 Å resolution Zika virus NS3 helicase crystal structure. ¹⁹ F NMR provided independent validation and also the direct observation of conformational tightening resulting from ssRNA binding in solution. The TSA stabilizes the two conformations of motif V of the helicase that link ATP hydrolysis with mechanical work. DFT analysis further validated the MgF ₃ (H ₂ O) ^- species, indicating the significance of this TSA for studies of biological motors.

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Organizational Affiliation: 

York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, United Kingdom.

Biological Assembly 1  

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: 51.29 kDa 
• Atom Count: 3,863 
• Modelled Residue Count: 441 
• Deposited Residue Count: 451 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A	451	Zika virus	Mutation(s): 0
UniProt
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)) Explore A0A024B7W1  Go to UniProtKB:  A0A024B7W1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	D [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF (Subject of Investigation/LOI)	C [auth A]	BERYLLIUM TRIFLUORIDE ION Be F3 OGIAHMCCNXDTIE-UHFFFAOYSA-K
MN (Subject of Investigation/LOI)	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.206 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.92	α = 90
b = 71.36	β = 93.73
c = 57.349	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-15 
Deposition Author(s): Ge, M., Molt Jr., R.W., Jenkins, H.T., Blackburn, G.M., Jin, Y., Antson, A.A.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	WT098230
Wellcome Trust	United Kingdom	WT101528

Revision History  

• Version 1.0: 2020-07-15
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-05-29
  Changes: Database references