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- PDB-7mmc: Crystal structure of HCV NS3/4A D168A protease in complex with NR... -

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Basic information

Entry
Database: PDB / ID: 7mmc
TitleCrystal structure of HCV NS3/4A D168A protease in complex with NR01-115
ComponentsNS3 protease
KeywordsHYDROLASE/INHIBITOR / NS3/4a Protease / Hepatitis C virus / Drug Resistance / Protease inhibitor / HYDROLASE-HYDROLASE Inhibitor complex / HYDROLASE / HYDROLASE-INHIBITOR complex / VIRAL PROTEIN
Function / homology
Function and homology information


transformation of host cell by virus / host cell membrane / serine-type peptidase activity / virion component / symbiont entry into host cell / virion attachment to host cell / proteolysis / membrane / metal ion binding
Similarity search - Function
Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-ZKA / NS3 protease
Similarity search - Component
Biological speciesHepacivirus C
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsZephyr, J. / Schiffer, C.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI085051 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31 GM131635 United States
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Deciphering the Molecular Mechanism of HCV Protease Inhibitor Fluorination as a General Approach to Avoid Drug Resistance.
Authors: Zephyr, J. / Nageswara Rao, D. / Vo, S.V. / Henes, M. / Kosovrasti, K. / Matthew, A.N. / Hedger, A.K. / Timm, J. / Chan, E.T. / Ali, A. / Kurt Yilmaz, N. / Schiffer, C.A.
History
DepositionApr 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,95015
Polymers21,3051
Non-polymers1,64514
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.330, 58.919, 96.208
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NS3 protease


Mass: 21305.152 Da / Num. of mol.: 1 / Mutation: D168A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepacivirus C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0B4WYC6

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Non-polymers , 5 types, 140 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ZKA / (1-methylcyclopropyl)methyl {(2R,4S,6S,12Z,13aS,14aR,16aS)-2-[(7-methoxy-3-methylquinoxalin-2-yl)oxy]-14a-[(1-methylcyclopropane-1-sulfonyl)carbamoyl]-5,16-dioxo-1,2,3,5,6,7,8,9,10,11,13a,14,14a,15,16,16a-hexadecahydrocyclopropa[e]pyrrolo[1,2-a][1,4]diazacyclopentadecin-6-yl}carbamate


Mass: 766.903 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H50N6O9S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES Buffer pH 6.5, 4% (W/V) Ammonium Sulfate, 20-26% PEG 3350 The cryogenic condition is 100 mM MES Buffer pH 6.5, 4% (W/V) Ammonium Sulfate, 20-26% PEG 3350, 15% Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.001→24.05 Å / Num. obs: 17311 / % possible obs: 95.95 % / Redundancy: 6 % / Biso Wilson estimate: 25.1 Å2 / CC1/2: 0.982 / Net I/σ(I): 15.25
Reflection shellResolution: 2.001→2.072 Å / Num. unique obs: 1466 / CC1/2: 0.975

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHASERphasing
HKL-3000703xdata scaling
Coot0.8.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VOJ

5voj


Resolution: 2.001→24.05 Å / SU ML: 0.1639 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.4054
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.214 866 5.01 %
Rwork0.1873 16436 -
obs0.1887 17302 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.59 Å2
Refinement stepCycle: LAST / Resolution: 2.001→24.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1419 0 105 126 1650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271604
X-RAY DIFFRACTIONf_angle_d0.83112183
X-RAY DIFFRACTIONf_chiral_restr0.0467249
X-RAY DIFFRACTIONf_plane_restr0.006279
X-RAY DIFFRACTIONf_dihedral_angle_d14.3066254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.130.23421300.20522475X-RAY DIFFRACTION87.98
2.13-2.290.23461420.1912693X-RAY DIFFRACTION96.56
2.29-2.520.27691440.19372735X-RAY DIFFRACTION97.17
2.52-2.880.1951440.19212749X-RAY DIFFRACTION96.95
2.88-3.630.20121480.18822805X-RAY DIFFRACTION98.2
3.63-24.70.20461580.17882979X-RAY DIFFRACTION99.08

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