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- PDB-3sv7: Crystal structure of NS3/4A protease variant R155K in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3sv7
TitleCrystal structure of NS3/4A protease variant R155K in complex with Telaprevir
ComponentsNS3 protease, NS4A protein
KeywordsVIRAL PROTEIN / HYDROLASE/INHIBITOR / NS3 / drug resistance / drug design / Protease inhibitors / HCV / serine protease / HYDROLASE / 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-SV6 / 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 12, 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 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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)22,3194
Polymers21,4751
Non-polymers8433
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.285, 58.823, 60.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein NS3 protease, NS4A protein


Mass: 21475.316 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, R1181K
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-SV6 / (1S,3aR,6aS)-2-[(2S)-2-({(2S)-2-cyclohexyl-2-[(pyrazin-2-ylcarbonyl)amino]acetyl}amino)-3,3-dimethylbutanoyl]-N-[(2R,3S)-1-(cyclopropylamino)-2-hydroxy-1-oxohexan-3-yl]octahydrocyclopenta[c]pyrrole-1-carboxamide / TELAPREVIR, bound form


Type: peptide-like / Mass: 681.865 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H55N7O6
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / 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.: 154 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTELAPREVIR IS A LINEAR, PEPTIDOMIMETIC HCV NS3/4A PROTEASE INHIBITOR FROM VERTEX. TELAPREVIR WAS ...TELAPREVIR IS A LINEAR, PEPTIDOMIMETIC HCV NS3/4A PROTEASE INHIBITOR FROM VERTEX. TELAPREVIR WAS FDA APPROVED FOR CLINICAL USE IN HUMANS. THE DRUG MIMICS THE PEPTIDE BACKBONE OF PROTEINS, ALTHOUGH THE DRUG MOIETIES CANNOT BE SEQUENCED USING AMINO ACID NOMENCLATURE
Sequence detailsTHE COFACTOR 4A RESIDUES 986-1000 (MET LYS LYS LYS GLY SER VAL VAL ILE VAL GLY ARG ILE ASN LEU) IN ...THE COFACTOR 4A RESIDUES 986-1000 (MET LYS LYS LYS GLY SER VAL VAL ILE VAL GLY ARG ILE ASN LEU) IN THIS ENTRY CORRESPOND TO RESIDUES NUMBERING 1674-1688 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: 2.29 Å3/Da / Density % sol: 46.2 %
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: Mar 31, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 29054 / % possible obs: 99.6 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.073 / Χ2: 1.001 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.55-1.616.40.46228231199.4
1.61-1.676.50.36828701.001199.5
1.67-1.756.50.27528331199.4
1.75-1.846.50.19529010.999199.7
1.84-1.956.50.15428671.001199.9
1.95-2.16.40.11628961.002199.9
2.1-2.326.30.09729030.9991100
2.32-2.656.20.07929281.0021100
2.65-3.3460.06229451.002199.8
3.34-505.90.05130881.001199

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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→33.51 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.2133 / WRfactor Rwork: 0.1787 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.883 / SU B: 2.87 / SU ML: 0.049 / SU R Cruickshank DPI: 0.074 / SU Rfree: 0.0774 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1986 1473 5.1 %RANDOM
Rwork0.1651 ---
obs0.1668 28901 99.21 %-
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: 95.69 Å2 / Biso mean: 24.7843 Å2 / Biso min: 12.58 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å20 Å20 Å2
2---1.27 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.55→33.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1432 0 55 154 1641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221541
X-RAY DIFFRACTIONr_bond_other_d0.0010.021004
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.9862112
X-RAY DIFFRACTIONr_angle_other_deg0.8453.0072407
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1385208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09322.85749
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24315222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5791510
X-RAY DIFFRACTIONr_chiral_restr0.080.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211730
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02295
X-RAY DIFFRACTIONr_mcbond_it0.6611.51010
X-RAY DIFFRACTIONr_mcbond_other0.1671.5419
X-RAY DIFFRACTIONr_mcangle_it1.23921624
X-RAY DIFFRACTIONr_scbond_it1.8843531
X-RAY DIFFRACTIONr_scangle_it3.1254.5481
LS refinement shellResolution: 1.55→1.592 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 111 -
Rwork0.205 1947 -
all-2058 -
obs--97.35 %
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)
1-0.212-2.2949-0.98552.57544.36645.57930.14260.04920.061-0.3042-0.1654-0.027-0.11350.06040.02270.413-0.02530.17130.1586-0.03480.16197.1075-19.9616-0.0411
20.96510.56910.82922.5188-1.07481.37960.0628-0.1350.04880.3547-0.06980.0102-0.29830.08960.0070.1298-0.030.02190.10250.00250.10512.21331.355323.3617
34.0386-0.7585-4.01593.45870.95646.24060.0521-0.10570.01210.0917-0.07810.01560.01490.12430.0260.101-0.0150.00070.07840.02610.09684.23264.591518.7989
43.9694-3.4661.70966.5752-2.25967.3340.1440.21170.0583-0.5835-0.288-0.3383-0.13650.25420.1440.10170.01060.07250.08710.02840.108510.5391-5.75279.0185
515.9696-0.4392-13.0011.22192.90615.3846-0.0702-0.3601-0.1245-0.07380.173-0.1894-0.33740.7219-0.10270.069-0.064-0.02630.12840.01980.164411.7994-2.293922.0814
61.2566-0.1628-0.3863.85660.51094.64490.16310.0894-0.049-0.1821-0.0928-0.0838-0.0968-0.0165-0.07030.0640.00910.00070.10960.00830.0860.024-4.983716.0526
71.042-0.3714-0.37080.54-0.05160.1880.01930.0648-0.04380.0247-0.025-0.0487-0.0265-0.0020.00570.09040.006-0.0010.10210.00540.1-2.1737-11.620920.9176
82.32431.1856-1.00161.6926-0.85531.06210.0727-0.1101-0.0841-0.0401-0.1369-0.14730.12480.15980.06420.06060.01720.00360.10480.00810.12937.2458-16.019218.0941
9-0.28410.344-0.27251.94040.50471.43410.04420.0639-0.04420.0806-0.0654-0.0270.0672-0.03530.02120.07160.01060.00550.1117-0.01490.1196-3.0695-17.796421.1973
1010.94541.5596-4.88141.5355-0.76413.49330.0303-0.5552-0.00540.0812-0.1113-0.146-0.16730.31640.0810.0624-0.0144-0.02050.12560.020.0692.9738-7.985231.5713
111.52510.1088-0.73590.0613-0.63994.50240.1179-0.23680.2468-0.021-0.05960.0670.01520.0743-0.05830.076-0.00810.02780.1197-0.03890.1186-13.0827-3.193533.0656
1211.80233.7541-6.0433.5943-5.57314.22260.14010.20040.4986-0.11860.15490.4083-0.31810.0159-0.29490.119-0.00480.03180.05780.02370.1574-8.38463.936621.6828
133.59421.1411-1.43813.0688-0.50010.8820.1274-0.02740.21740.13130.0001-0.0027-0.0682-0.0427-0.12750.0733-0.00170.02650.11510.0020.1165-20.2368-4.775831.1177
141.424-1.07920.13645.7439-3.75643.93810.06620.0666-0.0172-0.33640.12220.1077-0.1286-0.2188-0.18840.09790.01330.02730.14390.01460.1109-20.6998-4.331225.9313
1511.9108-6.01211.31720.0663-2.85923.7144-0.022-0.15480.49060.3130.098-0.1483-0.0429-0.2471-0.07590.08240.04590.03730.12030.0580.0817-16.07032.991616.5877
162.8833-2.327-0.01163.5992-0.75527.65730.16460.14-0.001-0.1532-0.15110.0459-0.1113-0.0552-0.01350.06850.00290.00870.11560.01270.1042-8.323-4.043119.0725
174.6972-1.958-3.86725.49764.296715.47540.2259-0.36940.3906-0.00710.1417-0.1395-0.05170.091-0.36770.0478-0.01410.02970.1358-0.04010.1381-8.8986-3.450935.0579
185.469-1.86193.56080.4936-0.56697.74030.1130.16960.0123-0.0397-0.15150.03940.05950.09470.03850.0875-0.00690.0070.1087-0.00410.1048-12.8973-8.593723.5366
192.59170.3482-4.6433.1288-3.9586.6080.15270.44160.00760.18570.36360.5779-0.0094-0.5944-0.51620.11580.0346-0.00160.24210.09610.1884-22.8968-2.599817.1189
207.442-5.24820.73174.7221-2.66572.8351-0.0312-0.1621-0.3232-0.03660.06850.25880.1899-0.0226-0.03730.1079-0.0158-0.00180.08520.01840.1209-8.9537-16.099329.3833
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A982 - 991
2X-RAY DIFFRACTION2A992 - 1004
3X-RAY DIFFRACTION3A1005 - 1012
4X-RAY DIFFRACTION4A1013 - 1025
5X-RAY DIFFRACTION5A1026 - 1031
6X-RAY DIFFRACTION6A1032 - 1041
7X-RAY DIFFRACTION7A1042 - 1061
8X-RAY DIFFRACTION8A1062 - 1076
9X-RAY DIFFRACTION9A1077 - 1087
10X-RAY DIFFRACTION10A1088 - 1097
11X-RAY DIFFRACTION11A1098 - 1108
12X-RAY DIFFRACTION12A1109 - 1114
13X-RAY DIFFRACTION13A1115 - 1120
14X-RAY DIFFRACTION14A1121 - 1129
15X-RAY DIFFRACTION15A1130 - 1135
16X-RAY DIFFRACTION16A1136 - 1142
17X-RAY DIFFRACTION17A1143 - 1149
18X-RAY DIFFRACTION18A1150 - 1158
19X-RAY DIFFRACTION19A1159 - 1167
20X-RAY DIFFRACTION20A1168 - 1179

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