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- PDB-6c2m: Crystal structure of HCV NS3/4A protease variant Y56H in complex ... -

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Basic information

Entry
Database: PDB / ID: 6c2m
TitleCrystal structure of HCV NS3/4A protease variant Y56H in complex with MK-5172
ComponentsNS3 protease
KeywordsHYDROLASE/HYDROLASE Inhibitor / NS3/4a Protease / Hepatitis C virus / Drug Resistance / protease inhibitor / HYDROLASE-HYDROLASE Inhibitor complex
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
Thrombin, subunit H - #120 / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-SUE / NS3 protease
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.859 Å
AuthorsMatthew, A.N. / 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 GM119345 United States
CitationJournal: To Be Published
Title: Clinical signature variant of HCV NS3/4A protease uses a novel mechanism to confer resistance
Authors: Matthew, A.N. / Schiffer, C.A.
History
DepositionJan 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NS3 protease
B: NS3 protease
C: NS3 protease
D: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,84413
Polymers83,4194
Non-polymers3,4259
Water3,765209
1
A: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6873
Polymers20,8551
Non-polymers8322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6873
Polymers20,8551
Non-polymers8322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7834
Polymers20,8551
Non-polymers9283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6873
Polymers20,8551
Non-polymers8322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.635, 103.326, 73.962
Angle α, β, γ (deg.)90.00, 112.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NS3 protease


Mass: 20854.637 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C1KIK8
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SUE / (1aR,5S,8S,10R,22aR)-5-tert-butyl-N-{(1R,2S)-1-[(cyclopropylsulfonyl)carbamoyl]-2-ethenylcyclopropyl}-14-methoxy-3,6-di oxo-1,1a,3,4,5,6,9,10,18,19,20,21,22,22a-tetradecahydro-8H-7,10-methanocyclopropa[18,19][1,10,3,6]dioxadiazacyclononadec ino[11,12-b]quinoxaline-8-carboxamide / Grazoprevir, MK-5172 / Grazoprevir


Mass: 766.903 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H50N6O9S / Comment: protease inhibitor*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES BUFFER PH 6.5, 4% (W/V) AMMONIUM SULFATE, 20-26% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.859→35.725 Å / Num. obs: 63506 / % possible obs: 96 % / Redundancy: 3.3 % / Rsym value: 0.066 / Net I/σ(I): 11.4
Reflection shellResolution: 1.859→1.906 Å / Rsym value: 0.281

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000703xdata scaling
PHASERphasing
Coot0.8.8model building
HKL-3000data collection
HKL-3000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VOJ

5voj


Resolution: 1.859→35.725 Å / Cross valid method: FREE R-VALUE / σ(F): 19.45 / Phase error: 29.44 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2242 1983 3.28 %
Rwork0.1805 --
obs0.1842 63486 95.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.859→35.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5382 0 225 211 5818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055738
X-RAY DIFFRACTIONf_angle_d0.8887892
X-RAY DIFFRACTIONf_dihedral_angle_d17.63322
X-RAY DIFFRACTIONf_chiral_restr0.051949
X-RAY DIFFRACTIONf_plane_restr0.005995
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8595-1.9060.25871400.24444277X-RAY DIFFRACTION91
1.906-1.95750.24561430.23294456X-RAY DIFFRACTION94
1.9575-2.0150.24761400.22314417X-RAY DIFFRACTION94
2.015-2.080.25781440.22064407X-RAY DIFFRACTION94
2.08-2.15430.25031360.21854438X-RAY DIFFRACTION94
2.1543-2.24040.24871410.21464449X-RAY DIFFRACTION94
2.2404-2.34230.25581360.2114426X-RAY DIFFRACTION94
2.3423-2.46560.26431520.2084429X-RAY DIFFRACTION93
2.4656-2.61980.23581390.2134354X-RAY DIFFRACTION93
2.6198-2.82170.22981410.19694392X-RAY DIFFRACTION92
2.8217-3.10490.23261480.18334383X-RAY DIFFRACTION92
3.1049-3.55240.2381430.16364371X-RAY DIFFRACTION92
3.5524-4.4690.18521380.13234299X-RAY DIFFRACTION91
4.469-21.45140.20041420.15794366X-RAY DIFFRACTION91

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