Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 26.33 kDa 
• Atom Count: 1663 
• Modelled Residue Count: 199 
• Deposited Residue Count: 247 
• Unique protein chains: 1

4M9K

NS2B-NS3 protease from dengue virus at pH 5.5

• PDB DOI: 10.2210/pdb4M9K/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Dengue virus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-08-14 Released: 2013-11-27 
• Deposition Author(s): Yildiz, M., Hardy, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.225 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Literature

Allosteric Inhibition of the NS2B-NS3 Protease from Dengue Virus.

Yildiz, M., Ghosh, S., Bell, J.A., Sherman, W., Hardy, J.A.

(2013) ACS Chem Biol 8: 2744-2752

• PubMed: 24164286 
• DOI: 10.1021/cb400612h
• Primary Citation of Related Structures:  
  4M9F, 4M9I, 4M9K, 4M9M, 4M9T


• PubMed Abstract: 
  

Dengue virus is the flavivirus that causes dengue fever, dengue hemorrhagic disease, and dengue shock syndrome, which are currently increasing in incidence worldwide. Dengue virus protease (NS2B-NS3pro) is essential for dengue virus infection and is thus a target of therapeutic interest. To date, attention has focused on developing active-site inhibitors of NS2B-NS3pro. The flat and charged nature of the NS2B-NS3pro active site may contribute to difficulties in developing inhibitors and suggests that a strategy of identifying allosteric sites may be useful. We report an approach that allowed us to scan the NS2B-NS3pro surface by cysteine mutagenesis and use cysteine reactive probes to identify regions of the protein that are susceptible to allosteric inhibition. This method identified a new allosteric site utilizing a circumscribed panel of just eight cysteine variants and only five cysteine reactive probes. The allosterically sensitive site is centered at Ala125, between the 120s loop and the 150s loop. The crystal structures of WT and modified NS2B-NS3pro demonstrate that the 120s loop is flexible. Our work suggests that binding at this site prevents a conformational rearrangement of the NS2B region of the protein, which is required for activation. Preventing this movement locks the protein into the open, inactive conformation, suggesting that this site may be useful in the future development of therapeutic allosteric inhibitors.

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Organizational Affiliation: 

Department of Chemistry, University of Massachusetts , 104 LGRT, 710 N. Pleasant St., Amherst, Massachussetts 01003, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS2B-NS3 protease	A	247	Dengue virus 2	Mutation(s): 0  Gene Names: dengue virus serotype 2 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)
UniProt
Find proteins for P12823 (Dengue virus type 2 (strain Puerto Rico/PR159-S1/1969)) Explore P12823  Go to UniProtKB:  P12823

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.225 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.503	α = 90
b = 62.019	β = 90
c = 114.114	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-14 
• Released Date: 2013-11-27 
Deposition Author(s): Yildiz, M., Hardy, J.A.

Revision History  

• Version 1.0: 2013-11-27
  Type: Initial release
  
• Version 1.1: 2014-02-05
  Changes: Database references
• Version 1.2: 2017-08-02
  Changes: Refinement description, Source and taxonomy