8Y9V

ZIKV NS2B/NS3 protease

• PDB DOI: https://doi.org/10.2210/pdb8Y9V/pdb

• Classification: HYDROLASE
• Organism(s): Zika virus, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-02-07 Released: 2024-02-28 
• Deposition Author(s): Zhang, C.Y., Xu, Q., Wang, W.W., Zhou, H., Wang, Q.S.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.248 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

Literature

Crystallographic data collection using a multilayer monochromator on an undulator beamline at SSRF

Zhang, C.Y., Xu, Q., Liang, M., Yu, L., Li, M.J., Zhu, Z.M., Huang, L.Q., Li, Q.H., Yu, F., Wang, Y.Z., Zhou, H., Wang, Q.S.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.95 kDa 
• Atom Count: 3,067 
• Modelled Residue Count: 387 
• Deposited Residue Count: 424 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease subunit NS2B	A, C	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
Serine protease NS3	B	153	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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease NS3	D	161	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

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DAR-LYS-ORN-ARG	E	4	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ORN	E	L-PEPTIDE LINKING	C5 H12 N2 O2		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.248 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.753	α = 90
b = 59.753	β = 90
c = 213.594	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-28 
Deposition Author(s): Zhang, C.Y., Xu, Q., Wang, W.W., Zhou, H., Wang, Q.S.

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Funding Organization	Location	Grant Number
Other government	China	21ZR1471800

Revision History  

• Version 1.0: 2024-02-28
  Type: Initial release