4A1V | pdb_00004a1v

Co-Complex structure of NS3-4A protease with the optimized inhibitory peptide CP5-46A-4D5E

• PDB DOI: https://doi.org/10.2210/pdb4A1V/pdb

• Classification: HYDROLASE/PEPTIDE
• Organism(s): Hepatitis C virus subtype 1b, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-09-20 Released: 2012-09-19 
• Deposition Author(s): Schmelz, S., Kuegler, J., Collins, J., Heinz, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

High Affinity Peptide Inhibitors of the Hepatitis C Virus Ns3-4A Protease Refractory to Common Resistant Mutants.

Kugler, J., Schmelz, S., Gentzsch, J., Haid, S., Pollmann, E., Van Den Heuvel, J., Franke, R., Pietschmann, T., Heinz, D.W., Collins, J.

(2012) J Biological Chem 287: 39224

• PubMed: 22965230 
• DOI: https://doi.org/10.1074/jbc.M112.393843
• Primary Citation Related Structures: 
  4A1T, 4A1V, 4A1X


• PubMed Abstract: 
  

  Hepatitis C virus (HCV) NS3-4A protease is essential for viral replication. All current small molecular weight drugs against NS3-4A are substrate peptidomimetics that have a similar binding and resistance profile. We developed inhibitory peptides (IPs) capping the active site and binding via a novel "tyrosine" finger at an alternative NS3-4A site that is of particular interest for further HCV drug development. The peptides are not cleaved due to a combination of geometrical constraints and impairment of the oxyanion hole function. Selection and optimization through combinatorial phagemid display, protein crystallography, and further modifications resulted in a 32-amino acid peptide with a K(i) of 0.53 nm. Inhibition of viral replication in cell culture was demonstrated by fusion to a cell-penetrating peptide. Negligible susceptibility to known (A156V and R155K) resistance mutations of the NS3-4A protease was observed. This work shows for the first time that antiviral peptides can target an intracellular site and reveals a novel druggable site on the HCV protease.

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Organizational Affiliation: 
• Research Group Directed Evolution, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany.

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 2  

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

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

Macromolecule Content 

• Total Structure Weight: 47.32 kDa 
• Atom Count: 3,161 
• Modeled Residue Count: 411 
• Deposited Residue Count: 446 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NON-STRUCTURAL PROTEIN 4A, SERINE PROTEASE NS3	A, B	203	Hepatitis C virus subtype 1b	Mutation(s): 2  EC: 3.4.21.98 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
Find proteins for P26662 (Hepatitis C virus genotype 1b (isolate Japanese)) Explore P26662  Go to UniProtKB:  P26662

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CP5-46A-4D5E	C, D	20	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	F [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	E [auth A], G [auth B], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.92	α = 90
b = 92.92	β = 90
c = 82.77	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-19 
Deposition Author(s): Schmelz, S., Kuegler, J., Collins, J., Heinz, D.W.

Revision History  

• Version 1.0: 2012-09-19
  Type: Initial release
  
• Version 1.1: 2012-11-21
  Changes: Database references, Structure summary
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description