5H4I | pdb_00005h4i

Unlinked NS2B-NS3 Protease from Zika Virus in complex with a compound fragment

• PDB DOI: https://doi.org/10.2210/pdb5H4I/pdb

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


• Deposited: 2016-10-31 Released: 2016-12-14 
• Deposition Author(s): Zhang, Z.Z., Li, Y.
• Funding Organization(s): NTU

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of unlinked NS2B-NS3 protease from Zika virus

Zhang, Z., Li, Y., Loh, Y.R., Phoo, W.W., Hung, A.W., Kang, C., Luo, D.

(2016) Science 354: 1597-1600

• PubMed: 27940580 
• DOI: https://doi.org/10.1126/science.aai9309
• Primary Citation Related Structures: 
  5GPI, 5H4I


• PubMed Abstract: 
  

  Zika virus (ZIKV) has rapidly emerged as a global public health concern. Viral NS2B-NS3 protease processes viral polyprotein and is essential for the virus replication, making it an attractive antiviral drug target. We report crystal structures at 1.58-angstrom resolution of the unlinked NS2B-NS3 protease from ZIKV as free enzyme and bound to a peptide reversely oriented at the active site. The unlinked NS2B-NS3 protease adopts a closed conformation in which NS2B engages NS3 to form an empty substrate-binding site. A second protease in the same crystal binds to the residues K14K15G16E17 from the neighboring NS3 in reverse orientation, resisting proteolysis. These features of ZIKV NS2B-NS3 protease may accelerate the discovery of structure-based antiviral drugs against ZIKV and related pathogenic flaviviruses.

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Organizational Affiliation: 
• Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building 03-07, 59 Nanyang Drive, Singapore 636921.
NTU Institute of Structural Biology, Nanyang Technological University, Experimental Medicine Building 06-01, 59 Nanyang Drive, Singapore 636921.
Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669.
School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.
Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669. [e-mail] [e-mail].
Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building 03-07, 59 Nanyang Drive, Singapore 636921. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 25.1 kDa 
• Atom Count: 1,511 
• Modeled Residue Count: 193 
• Deposited Residue Count: 231 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS2B cofactor	A	53	Zika virus	Mutation(s): 0
UniProt
Find proteins for H8XX12 (Zika virus) Explore H8XX12  Go to UniProtKB:  H8XX12

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NS3 protease	B	178	Zika virus	Mutation(s): 0
UniProt
Find proteins for H8XX12 (Zika virus) Explore H8XX12  Go to UniProtKB:  H8XX12

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7HQ	C [auth B]	benzimidazol-1-ylmethanol C8 H8 N2 O IWCRZZKSGBFRSJ-UHFFFAOYSA-N
ACT	D [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.345	α = 90
b = 42.345	β = 90
c = 214.998	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-12-14 
Deposition Author(s): Zhang, Z.Z., Li, Y.

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Funding Organization	Location	Grant Number
NTU	Singapore	START UP GRANT

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2017-01-25
  Changes: Database references
• Version 1.2: 2020-02-26
  Changes: Data collection
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary