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- PDB-3su3: Crystal structure of NS3/4A protease in complex with vaniprevir -

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Basic information

Entry
Database: PDB / ID: 3su3
TitleCrystal structure of NS3/4A protease in complex with vaniprevir
ComponentsNS3 protease, NS4A protein
KeywordsHYDROLASE/INHIBITOR / drug resistance / drug design / Protease inhibitors / serine protease / VIRAL PROTEIN / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / channel activity / viral nucleocapsid ...host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / channel activity / viral nucleocapsid / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Thrombin, subunit H - #120 / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily ...Thrombin, subunit H - #120 / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily / : / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / : / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / NS3 RNA helicase, C-terminal helical domain / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Trypsin-like serine proteases / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Thrombin, subunit H / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chem-SU3 / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSchiffer, C.A. / Romano, K.P.
CitationJournal: Plos Pathog. / Year: 2012
Title: The Molecular Basis of Drug Resistance against Hepatitis C Virus NS3/4A Protease Inhibitors.
Authors: Romano, K.P. / Ali, A. / Aydin, C. / Soumana, D. / Ozen, A. / Deveau, L.M. / Silver, C. / Cao, H. / Newton, A. / Petropoulos, C.J. / Huang, W. / Schiffer, C.A.
History
DepositionJul 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NS3 protease, NS4A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5035
Polymers21,4871
Non-polymers1,0154
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.095, 58.461, 60.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NS3 protease, NS4A protein


Mass: 21487.330 Da / Num. of mol.: 1
Fragment: NS4A (UNP residues 1674-1688), NS3 (UNP residues 1027-1208)
Mutation: A1027S, P1028G, I1029D, L1039E, L1040E, I1043Q, I1044E, L1047Q, A1066T, C1073S, C1078L, I1098T, P1112Q, S1165A, C1185S, C1679S, V1686I, I1687N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Strain: subtype 1a, BID-V318 / Gene: NS3-NS4A / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8DG50
#2: Chemical ChemComp-SU3 / (5R,7S,10S)-10-tert-butyl-N-{(1R,2R)-1-[(cyclopropylsulfonyl)carbamoyl]-2-ethylcyclopropyl}-15,15-dimethyl-3,9,12-trioxo-6,7,9,10,11,12,14,15,16,17,18,19-dodecahydro-1H,5H-2,23:5,8-dimethano-4,13,2,8,11-benzodioxatriazacyclohenicosine-7(3H)-carboxamide / vaniprevir / MK-7009


Mass: 757.936 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H55N5O9S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsVANIPREVIR (MK-7009) IS A MACROCYCLIC, PEPTIDOMIMETIC HCV NS3/4A PROTEASE INHIBITOR FROM MERCK. THE ...VANIPREVIR (MK-7009) IS A MACROCYCLIC, PEPTIDOMIMETIC HCV NS3/4A PROTEASE INHIBITOR FROM MERCK. THE DRUG MIMICS THE PEPTIDE BACKBONE OF PROTEINS, ALTHOUGH THE DRUG MOIETIES CANNOT BE SEQUENCED USING AMINO ACID NOMENCLATURE.
Sequence detailsTHE COFACTOR 4A RESIDUES 990-1000 (GLY SER VAL VAL ILE VAL GLY ARG ILE ASN LEU) IN THIS ENTRY ...THE COFACTOR 4A RESIDUES 990-1000 (GLY SER VAL VAL ILE VAL GLY ARG ILE ASN LEU) IN THIS ENTRY CORRESPOND TO RESIDUES NUMBERING 1678-1688 OF DATABASE SEQUENCE REFERENCE (UNP A8DG50). THIS PEPTIDE IS COVALENTLY LINKED TO THE N-TERMINUS OF NS3. C1679S MUTATION WAS ENGINEERED TO PREVENT DISULFIDE FORMATION. THE V1686I AND I1687N WERE ENGINEERED TO OPTIMIZE THE LINKER BETWEEN THE COFACTOR 4A AND NS3.

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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: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 295 K / Method: hanging drop, vapor diffusion / pH: 6.2
Details: 20-25% PEG 3350, 0.1M MES (pH 6.5), 4% ammonium sulfate, hanging drop, vapor diffusion, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorDate: Dec 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 46251 / % possible obs: 95.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.052 / Χ2: 1.003 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.3-1.353.70.32940561.002185.7
1.35-1.44.10.25345311.007195
1.4-1.464.10.20545361195
1.46-1.544.20.15545731.003195.3
1.54-1.644.30.12145661196
1.64-1.764.40.09946781.005197.2
1.76-1.944.40.07447261.002198.2
1.94-2.224.40.06148001.003198.7
2.22-2.84.30.05248251.006198.9
2.8-504.20.03149601.005197.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→33.38 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.1928 / WRfactor Rwork: 0.178 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9011 / SU B: 1.339 / SU ML: 0.029 / SU R Cruickshank DPI: 0.0485 / SU Rfree: 0.0493 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1823 2344 5.1 %RANDOM
Rwork0.1644 ---
obs0.1653 46084 95.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 51.78 Å2 / Biso mean: 16.9941 Å2 / Biso min: 6.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å20 Å2
2---0.61 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.3→33.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1468 0 64 212 1744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221584
X-RAY DIFFRACTIONr_bond_other_d0.0010.021051
X-RAY DIFFRACTIONr_angle_refined_deg1.4452.0012171
X-RAY DIFFRACTIONr_angle_other_deg0.8113.0062524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1395207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.6823.21456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86615245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5291512
X-RAY DIFFRACTIONr_chiral_restr0.0790.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211758
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02297
X-RAY DIFFRACTIONr_mcbond_it0.6211.51010
X-RAY DIFFRACTIONr_mcbond_other0.1711.5419
X-RAY DIFFRACTIONr_mcangle_it1.12921631
X-RAY DIFFRACTIONr_scbond_it1.7493574
X-RAY DIFFRACTIONr_scangle_it2.7184.5530
LS refinement shellResolution: 1.3→1.336 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 141 -
Rwork0.235 2708 -
all-2849 -
obs--80.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.55272.5546-3.6978-0.32756.015415.37350.2691-0.1366-0.2441-0.0559-0.0594-0.0526-0.5109-0.0888-0.20980.155-0.00140.06130.0520.03910.05797.8677-21.5612-3.883
20.5820.0279-1.19854.35181.52552.7668-0.0740.0475-0.0072-0.19690.1046-0.18630.02880.1201-0.03070.06110.00160.01060.0698-0.00180.06295.2261-7.466913.5543
33.1325-0.5496-2.84432.93670.10354.70560-0.18010.0990.14620.0549-0.0171-0.02150.1231-0.05490.0645-0.0066-0.00670.0402-0.00180.05152.46625.419622.3645
43.3152-1.0640.23996.42431.26176.1714-0.06610.09720.0858-0.51990.1105-0.6181-0.24520.3887-0.04440.089-0.02340.09820.0191-0.00330.081311.7934-5.885111.5546
517.6272.4143-3.79063.3992-1.09224.70260.0741-0.32990.34710.1246-0.0811-0.1944-0.15180.27970.0070.0708-0.0189-0.01250.036-0.00610.07435.7435-1.481626.2764
61.39741.15151.26343.11822.490211.05350.0880.17-0.0059-0.12290.0291-0.09680.2052-0.0008-0.11710.05080.00950.00160.07390.00290.05290.1279-5.172812.9615
71.832-1.16211.22321.0559-1.8245.21940.00210.04590.03680.03960.0058-0.0285-0.0148-0.0103-0.00790.0522-0.00820.00080.04640.0010.051-1.8723-6.432421.191
81.1203-0.08090.21381.07210.29690.6473-0.0021-0.0102-0.04960.0551-0.0057-0.04140.0677-0.01210.00780.05530.00650.00260.0490.00610.0531-2.1623-13.743320.2806
91.22420.6401-0.16791.9864-0.37241.00840.0723-0.0630.0104-0.0101-0.0456-0.17580.05390.1251-0.02670.0370.01730.00820.0643-0.00990.07338.8726-14.539117.206
102.12970.3491-0.1480.4590.48720.30630.0270.0146-0.07940.1032-0.0245-0.00970.0778-0.0201-0.00250.060.0048-0.00070.05320.00060.062-4.178-18.453720.6128
114.6577-0.5562-0.77794.32432.37112.91660.1321-0.01840.14550.00060.0389-0.34-0.07020.1232-0.1710.0592-0.0042-0.02580.05980.01780.05136.8485-8.499928.4025
1211.0617-2.8474-3.96151.39011.47096.4816-0.1415-0.126-0.10970.0884-0.13640.11170.07230.08460.27790.04150.00470.01550.1049-0.01130.0594-9.2102-9.302938.8782
133.68761.7459-3.66640.7486-2.23085.71570.1065-0.1080.20850.0166-0.01750.1072-0.11460.0708-0.0890.06290.00270.02220.043-0.01440.0895-11.08171.366226.373
141.21060.0056-1.26173.021-0.94870.95630.0014-0.04950.0165-0.01130.0231-0.0072-0.00920.0209-0.02450.026-0.00340.01420.0685-0.00790.0562-19.4769-7.730930.5642
152.08020.5744-0.77744.7109-2.09121.82490.13030.04420.18910.11330.02040.2061-0.1848-0.1226-0.15070.07110.01440.03740.07880.00580.0615-21.279-1.563725.4825
1612.8387-4.74552.27833.8125-3.38925.5397-0.1118-0.30820.3660.38790.3695-0.0459-0.2081-0.4207-0.25770.11420.04690.03650.12860.03420.0924-16.19972.649516.8256
170.2385-0.1139-0.32320.1717-0.23162.77580.0266-0.05250.08070.02340.01910.1018-0.0895-0.0751-0.04570.0547-0.00440.00550.0719-0.00260.0727-8.7609-3.957922.4136
181.0973-0.3022-0.64670.31710.35811.14470.0003-0.07340.08110.00170.00040.0206-0.01740.0668-0.00070.0476-0.00630.01640.0542-0.00790.0483-11.3126-6.782328.3715
193.3531-1.47771.34982.8555-2.57973.18890.0120.04570.04570.01290.14550.1684-0.0364-0.2079-0.15740.0499-0.00630.01950.06530.010.0555-18.2749-6.947521.6198
2016.90720.1198-9.91092.5299-0.17926.0826-0.6773-0.8013-0.7356-0.12210.09990.12090.51420.24730.57740.1720.04890.02790.06970.05430.0771-6.2104-18.881230.8942
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A982 - 987
2X-RAY DIFFRACTION2A988 - 997
3X-RAY DIFFRACTION3A998 - 1014
4X-RAY DIFFRACTION4A1015 - 1027
5X-RAY DIFFRACTION5A1028 - 1033
6X-RAY DIFFRACTION6A1034 - 1041
7X-RAY DIFFRACTION7A1042 - 1048
8X-RAY DIFFRACTION8A1049 - 1061
9X-RAY DIFFRACTION9A1062 - 1074
10X-RAY DIFFRACTION10A1075 - 1085
11X-RAY DIFFRACTION11A1086 - 1094
12X-RAY DIFFRACTION12A1095 - 1101
13X-RAY DIFFRACTION13A1102 - 1114
14X-RAY DIFFRACTION14A1115 - 1122
15X-RAY DIFFRACTION15A1123 - 1129
16X-RAY DIFFRACTION16A1130 - 1135
17X-RAY DIFFRACTION17A1136 - 1144
18X-RAY DIFFRACTION18A1145 - 1158
19X-RAY DIFFRACTION19A1159 - 1172
20X-RAY DIFFRACTION20A1173 - 1179

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