5GJ4

Structure of NS2B-NS3 Protease from Zika Virus caught after self-cleavage


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the NS2B-NS3 protease from Zika virus after self-cleavage.

Phoo, W.W.Li, Y.Zhang, Z.Lee, M.Y.Loh, Y.R.Tan, Y.B.Ng, E.Y.Lescar, J.Kang, C.Luo, D.

(2016) Nat Commun 7: 13410-13410

  • DOI: 10.1038/ncomms13410
  • Primary Citation of Related Structures:  
    5GJ4

  • PubMed Abstract: 
  • The recent outbreak of Zika virus (ZIKV) infections in the Americas represents a serious threat to the global public health. The viral protease that processes viral polyproteins during infection appears as an attractive drug target. Here we report a crystal structure at 1 ...

    The recent outbreak of Zika virus (ZIKV) infections in the Americas represents a serious threat to the global public health. The viral protease that processes viral polyproteins during infection appears as an attractive drug target. Here we report a crystal structure at 1.84 Å resolution of ZIKV non-structural protein NS2B-NS3 protease with the last four amino acids of the NS2B cofactor bound at the NS3 active site. This structure represents a post-proteolysis state of the enzyme during viral polyprotein processing and provides insights into peptide substrate recognition by the protease. Nuclear magnetic resonance (NMR) studies and protease activity assays unravel the protein dynamics upon binding the protease inhibitor BPTI in solution and confirm this finding. The structural and functional insights of the ZIKV protease presented here should advance our current understanding of flavivirus replication and accelerate structure-based antiviral drug discovery against ZIKV.


    Organizational Affiliation

    NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine protease subunit NS2BA, C, E, G61Zika virusMutation(s): 0 
EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
Find proteins for Q32ZE1 (Zika virus)
Explore Q32ZE1 
Go to UniProtKB:  Q32ZE1
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Serine protease NS3B, D, F, H177Zika virusMutation(s): 0 
EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
Find proteins for Q32ZE1 (Zika virus)
Explore Q32ZE1 
Go to UniProtKB:  Q32ZE1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth B], J [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.181 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.79α = 90
b = 88.79β = 90
c = 138.1γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata processing
Aimlessdata scaling
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-06-27 
  • Released Date: 2016-10-26 
  • Deposition Author(s): Phoo, W.W., Li, Y.

Funding OrganizationLocationGrant Number
NMRCSingaporeCBRG14May051

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-12-07
    Changes: Database references