5Y4Z | pdb_00005y4z

Crystal structure of the Zika virus NS3 helicase complex with AMPPNP

• PDB DOI: https://doi.org/10.2210/pdb5Y4Z/pdb

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


• Deposited: 2017-08-06 Released: 2017-08-30 
• Deposition Author(s): Li, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Structural view of the helicase reveals that Zika virus uses a conserved mechanism for unwinding RNA

Li, L., Wang, J., Jia, Z., Shaw, N.

(2018) Acta Crystallogr F Struct Biol Commun 74: 205-213

• DOI: https://doi.org/10.1107/S2053230X18003813

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.07 kDa 
• Atom Count: 3,929 
• Modeled Residue Count: 440 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS3 helicase	A	440	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)
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
ANP	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MN (Subject of Investigation/LOI)	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.754	α = 90
b = 68.779	β = 92.5
c = 56.971	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data processing
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-30 
Deposition Author(s): Li, L.

Revision History  

• Version 1.0: 2017-08-30
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references, Derived calculations