4OOW | pdb_00004oow

HCV NS5B polymerase with a fragment of quercetagetin

• PDB DOI: https://doi.org/10.2210/pdb4OOW/pdb

• Classification: TRANSFERASE
• Organism(s): Hepatitis C virus isolate HC-J4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-02-04 Released: 2014-12-17 
• Deposition Author(s): Guichou, J.F., Ahmed-Belkacem, A., Rozenn, B., Nazim, N., Hernandez, E., Pallier, C., Pawlotsky, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 
  0.277 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Inhibition of RNA binding to hepatitis C virus RNA-dependent RNA polymerase: a new mechanism for antiviral intervention.

Ahmed-Belkacem, A., Guichou, J.F., Brillet, R., Ahnou, N., Hernandez, E., Pallier, C., Pawlotsky, J.M.

(2014) Nucleic Acids Res 42: 9399-9409

• PubMed: 25053847 
• DOI: https://doi.org/10.1093/nar/gku632
• Primary Citation Related Structures: 
  4OOW


• PubMed Abstract: 
  

  The hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp) is a key target for antiviral intervention. The goal of this study was to identify the binding site and unravel the molecular mechanism by which natural flavonoids efficiently inhibit HCV RdRp. Screening identified the flavonol quercetagetin as the most potent inhibitor of HCV RdRp activity. Quercetagetin was found to inhibit RdRp through inhibition of RNA binding to the viral polymerase, a yet unknown antiviral mechanism. X-ray crystallographic structure analysis of the RdRp-quercetagetin complex identified quercetagetin's binding site at the entrance of the RNA template tunnel, confirming its original mode of action. This antiviral mechanism was associated with a high barrier to resistance in both site-directed mutagenesis and long-term selection experiments. In conclusion, we identified a new mechanism for non-nucleoside inhibition of HCV RdRp through inhibition of RNA binding to the enzyme, a mechanism associated with broad genotypic activity and a high barrier to resistance. Our results open the way to new antiviral approaches for HCV and other viruses that use an RdRp based on RNA binding inhibition, that could prove to be useful in human, animal or plant viral infections.

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Organizational Affiliation: 
• Inserm U955, Hôpital Henri Mondor, 51 avenue du Maréchal de Lattre de Tassigny, 94010 Créteil, France.
Centre de Biochimie Structurale, Inserm U1054, CNRS UMR5048, Universités Montpellier 1 et 2, 29 rue de Navacelles, 34090 Montpellier, France.
Inserm U955, Hôpital Henri Mondor, 51 avenue du Maréchal de Lattre de Tassigny, 94010 Créteil, France Department of Virology, Hôpital Paul Brousse, 12 avenue Paul Vaillant Couturier, 94800 Villejuif, France.
Inserm U955, Hôpital Henri Mondor, 51 avenue du Maréchal de Lattre de Tassigny, 94010 Créteil, France National Reference Center for Viral Hepatitis B, C, and Delta, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, 51 avenue du Maréchal de Lattre de Tassigny, 94010 Créteil, France [e-mail].

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 129.17 kDa 
• Atom Count: 8,841 
• Modeled Residue Count: 1,093 
• Deposited Residue Count: 1,156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase	A, B	578	Hepatitis C virus isolate HC-J4	Mutation(s): 0  EC: 2.7.7.48
UniProt
Find proteins for O92972 (Hepatitis C virus genotype 1b (strain HC-J4)) Explore O92972  Go to UniProtKB:  O92972

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAQ	C [auth A]	CATECHOL C6 H6 O2 YCIMNLLNPGFGHC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free:  0.277 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.6	α = 90
b = 108.87	β = 90
c = 134.97	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-17 
Deposition Author(s): Guichou, J.F., Ahmed-Belkacem, A., Rozenn, B., Nazim, N., Hernandez, E., Pallier, C., Pawlotsky, J.M.

Revision History  

• Version 1.0: 2014-12-17
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description