6S0J | pdb_00006s0j

Structure of Zika virus NS3 helicase in complex with ADP-MgF3(H2O)-

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.189 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.145 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 
    0.147 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6S0J

Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history. 

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

  • DOI: https://doi.org/10.1021/acscatal.0c04500
  • Primary Citation 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.

    • Organizational Affiliation: 
    • York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 51.29 kDa 
  • Atom Count: 3,935 
  • Modeled Residue Count: 433 
  • Deposited Residue Count: 451 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Genome polyprotein451Zika virusMutation(s): 0 
UniProt
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013))
Explore A0A024B7W1 
Go to UniProtKB:  A0A024B7W1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A024B7W1
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.189 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.145 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 0.147 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.943α = 90
b = 69.604β = 94.4
c = 57.751γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomWT098230
Wellcome TrustUnited KingdomWT101528

Revision History  (Full details and data files)

  • 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
  • Version 2.0: 2025-11-19
    Changes: Non-polymer description, Structure summary