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- PDB-3su5: Crystal structure of NS3/4A protease variant D168A in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3su5
TitleCrystal structure of NS3/4A protease variant D168A 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 suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / 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 / lipid droplet / protein complex oligomerization ...host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / 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 / lipid droplet / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / 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 / induction by virus of host autophagy / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / zinc ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Thrombin, subunit H - #120 / : / Hepatitis C virus core protein, chain A superfamily / 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 ...Thrombin, subunit H - #120 / : / Hepatitis C virus core protein, chain A superfamily / 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 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 / 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: 1.55 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

Downloads & links

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Assembly

Deposited unit
A: NS3 protease, NS4A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6517
Polymers21,4431
Non-polymers1,2086
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.066, 58.538, 60.015
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: 21443.320 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, D1194A
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 / Comment: protease inhibitor*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / 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.: 180 / 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: 45.46 %
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: 1.55→50 Å / Num. obs: 27508 / % possible obs: 95.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.09 / Χ2: 1.003 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.55-1.616.80.50626181193
1.61-1.676.80.41126481.001192.9
1.67-1.756.80.32626321.004194.2
1.75-1.846.70.24126801.003194.6
1.84-1.956.70.18627261.006195.7
1.95-2.16.90.13727290.999196.5
2.1-2.327.20.11127881.005197.1
2.32-2.657.30.09528071.004197.5
2.65-3.347.30.07128691.002198.3
3.34-506.80.05330111198.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→30.01 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.1962 / WRfactor Rwork: 0.1733 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.887 / SU B: 2.664 / SU ML: 0.048 / SU R Cruickshank DPI: 0.0794 / SU Rfree: 0.0756 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1831 1386 5.1 %RANDOM
Rwork0.1648 ---
obs0.1657 27380 95.26 %-
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: 57.05 Å2 / Biso mean: 18.8719 Å2 / Biso min: 8.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.95 Å20 Å20 Å2
2---0.63 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 74 180 1693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221576
X-RAY DIFFRACTIONr_bond_other_d0.0010.021020
X-RAY DIFFRACTIONr_angle_refined_deg1.3912.0052169
X-RAY DIFFRACTIONr_angle_other_deg0.8223.0062449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2295209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34522.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.83115228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.141511
X-RAY DIFFRACTIONr_chiral_restr0.0790.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211748
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02302
X-RAY DIFFRACTIONr_mcbond_it0.5211.51014
X-RAY DIFFRACTIONr_mcbond_other0.1381.5419
X-RAY DIFFRACTIONr_mcangle_it0.92921631
X-RAY DIFFRACTIONr_scbond_it1.5553562
X-RAY DIFFRACTIONr_scangle_it2.3894.5527
LS refinement shellResolution: 1.55→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 111 -
Rwork0.224 1733 -
all-1844 -
obs--88.44 %
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)
16.9069-1.1273-1.04246.574513.278324.28850.2827-0.1433-0.2946-0.262-0.41540.2613-0.3396-0.64260.13260.1695-0.01140.05760.11220.04050.0987.4131-21.7425-3.1669
20.98350.1272-1.31815.34031.58912.285-0.05740.01460.0051-0.18990.1285-0.1344-0.06830.1337-0.07110.0477-0.00040.00970.0886-0.00640.08784.9139-6.020314.6801
33.44080.6853-3.38171.32650.09234.06990.1016-0.31630.13520.2429-0.0221-0.0111-0.17510.2913-0.07950.1230.0064-0.00690.0828-0.00570.07490.84166.569425.4691
43.3037-1.7876-3.461118.81533.33291.4735-0.3172-0.06850.027-1.19580.2613-0.5660.0644-0.02430.0560.25610.00020.08360.0515-0.01780.05488.6834-0.42939.3773
51.54871.45932.88947.69433.064811.2562-0.1297-0.0270.053-0.47550.0604-0.5477-0.22470.16390.06920.0564-0.00570.08730.0605-0.02060.121512.6264-6.648312.389
619.35561.9079-5.93183.52950.33286.9959-0.0196-0.51960.33010.16980.0104-0.1602-0.20430.29320.00930.0702-0.0219-0.02360.04120.00470.07235.6921-1.492226.1727
72.43580.74861.10362.0304-0.134.8870.07880.1854-0.0498-0.12560.0615-0.06380.1748-0.0633-0.14030.04860.01140.00130.08490.0110.0707-0.3061-4.78712.749
80.9552-0.04970.26181.23270.20450.3509-0.00380.0073-0.01640.0413-0.0041-0.04480.00020.01560.00790.05370.00680.00480.06860.00590.0692-2.1419-11.246421.5511
91.36551.9616-0.45595.31411.50670.91460.0477-0.0322-0.01770.0112-0.0164-0.08120.02320.014-0.03140.05750.02080.00590.0766-0.00180.09485.7889-13.758914.3525
100.14980.1164-0.0421.0276-0.05820.73110.0237-0.0351-0.04440.0389-0.0278-0.06860.04220.05270.00410.06220.0126-0.00380.0703-0.00030.07971.562-17.180920.1929
1111.63411.3186-7.52181.2644-0.39695.6966-0.1054-0.5833-0.14730.0378-0.1027-0.08380.00370.28920.20810.05880.0154-0.01870.1070.01140.0532-0.1198-8.154533.5571
123.71821.9381-3.82330.9281-2.40896.57170.1001-0.08350.24020.0404-0.00230.1036-0.1290.0421-0.09780.05540.00330.02330.071-0.01370.0965-11.35120.909226.8699
131.77970.1949-1.20641.2119-0.71071.90160.0308-0.0176-0.0042-0.01930.04280.03020.0266-0.0463-0.07360.0495-0.0050.01380.09030.00260.0831-20.0357-7.118529.4258
141.66611.68967.19080.27061.625840.7887-0.34530.03550.37110.2235-0.347-0.2589-0.93390.98560.69230.1386-0.0344-0.00450.15060.12410.3435-20.72393.229423.4736
151.0323-0.4961-0.34581.6719-1.99261.88270.09310.01770.09420.09150.11530.0705-0.1314-0.1538-0.20840.08280.01790.01290.09470.00740.0983-12.53850.368917.3476
162.7948-1.2164-5.19192.84733.2079.91750.1715-0.20750.26320.0329-0.0012-0.0657-0.01860.2163-0.17030.079-0.02290.06250.1123-0.05280.1111-8.9564-3.375535.0036
171.1675-0.4808-0.21340.21920.62722.0180.0181-0.049-0.01880.0111-0.03440.04460.0219-0.0340.01630.0581-0.01530.00560.07410.00350.0734-12.8053-8.759323.5214
187.14956.9286-4.23813.5501-5.305724.1280.06120.61270.55180.17090.65190.5798-0.2608-1.5557-0.71310.04070.07430.00540.21550.11840.186-24.2234-1.819215.7723
194.6321-3.06633.26332.878-2.54364.43930.0027-0.1416-0.1430.11140.12810.08860.0379-0.0792-0.13070.0637-0.01040.00880.07370.01950.0696-13.057-12.204827.3734
2021.1827-0.71232.22248.69336.2592.9198-0.4104-1.0706-0.9830.70030.20570.16170.49080.0110.20470.19710.06820.14470.09510.14150.223-4.3145-21.117830.8838
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A981 - 988
2X-RAY DIFFRACTION2A989 - 997
3X-RAY DIFFRACTION3A998 - 1010
4X-RAY DIFFRACTION4A1011 - 1017
5X-RAY DIFFRACTION5A1018 - 1027
6X-RAY DIFFRACTION6A1028 - 1033
7X-RAY DIFFRACTION7A1034 - 1042
8X-RAY DIFFRACTION8A1043 - 1060
9X-RAY DIFFRACTION9A1061 - 1066
10X-RAY DIFFRACTION10A1067 - 1087
11X-RAY DIFFRACTION11A1088 - 1100
12X-RAY DIFFRACTION12A1101 - 1114
13X-RAY DIFFRACTION13A1115 - 1125
14X-RAY DIFFRACTION14A1126 - 1130
15X-RAY DIFFRACTION15A1131 - 1142
16X-RAY DIFFRACTION16A1143 - 1149
17X-RAY DIFFRACTION17A1150 - 1158
18X-RAY DIFFRACTION18A1159 - 1165
19X-RAY DIFFRACTION19A1166 - 1174
20X-RAY DIFFRACTION20A1175 - 1181

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