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- PDB-3su2: Crystal structure of NS3/4A protease variant A156T in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3su2
TitleCrystal structure of NS3/4A protease variant A156T in complex with danoprevir
ComponentsGenome polyprotein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / NS3 / drug resistance / drug design / Protease inhibitors / HCV / serine protease / HYDROLASE / HYDROLASE-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 / symbiont-mediated transformation of host cell / 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 suppression of host TRAF-mediated signal transduction / symbiont-mediated transformation of host cell / 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 / 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 / Trypsin-like serine proteases / 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-TSV / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus subtype 1a
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.496 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 2, 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 1.3Jan 18, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_entity_nonpoly.name / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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
Revision 1.4Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5055
Polymers21,5171
Non-polymers9874
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.885, 58.528, 59.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Genome polyprotein


Mass: 21517.355 Da / Num. of mol.: 1 / Mutation: C1679S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus subtype 1a / Strain: BID-V318 / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8DG50
#2: Chemical ChemComp-TSV / (2R,6S,12Z,13aS,14aR,16aS)-6-[(tert-butoxycarbonyl)amino]-14a-[(cyclopropylsulfonyl)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-2-yl 4-fluoro-2H-isoindole-2-carboxylate / ITMN-191 / danoprevir


Mass: 729.815 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H44FN5O9S / Comment: inhibitor*YM
#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.: 176 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45.05 %
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
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.496→50 Å / Num. obs: 31822 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.065 / Χ2: 1.002 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.496-1.557.10.50231271.0011100
1.55-1.627.20.3731201.0011100
1.62-1.697.20.28931291.0051100
1.69-1.787.30.21831541.0031100
1.78-1.897.30.1531491.0021100
1.89-2.047.20.10331641.0021100
2.04-2.247.20.0831761.0041100
2.24-2.567.20.074318211100
2.56-3.237.20.05532411.0041100
3.23-506.90.02733801199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M5M CHAIN B

3m5m


Resolution: 1.496→40.49 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.1847 / WRfactor Rwork: 0.1604 / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.9027 / SU B: 2.014 / SU ML: 0.039 / SU R Cruickshank DPI: 0.0633 / SU Rfree: 0.0642 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1772 1603 5.1 %RANDOM
Rwork0.1539 ---
obs0.1551 31646 99.39 %-
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: 58.14 Å2 / Biso mean: 17.4773 Å2 / Biso min: 7.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20 Å2
2---0.77 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.496→40.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1411 0 62 176 1649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211545
X-RAY DIFFRACTIONr_bond_other_d0.0010.021008
X-RAY DIFFRACTIONr_angle_refined_deg1.3992.0082125
X-RAY DIFFRACTIONr_angle_other_deg1.03632475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3885209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96522.65349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03515228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6571511
X-RAY DIFFRACTIONr_chiral_restr0.0760.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211739
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02303
X-RAY DIFFRACTIONr_mcbond_it0.5871.5995
X-RAY DIFFRACTIONr_mcbond_other0.1581.5413
X-RAY DIFFRACTIONr_mcangle_it1.07721601
X-RAY DIFFRACTIONr_scbond_it1.7073550
X-RAY DIFFRACTIONr_scangle_it2.5374.5512
LS refinement shellResolution: 1.496→1.535 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 114 -
Rwork0.193 2138 -
all-2252 -
obs--96.9 %
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)
17.6744-3.39290.648519.871119.897520.56820.6269-0.00260.0807-0.9507-0.4583-0.3294-0.7431-0.6101-0.16860.2412-0.00910.14850.04210.02060.06937.5081-21.084-2.6541
21.5162-0.635-1.0463.81631.6462.55930.0451-0.11110.07540.17470.0533-0.1535-0.10940.1023-0.09840.0712-0.00450.00650.03740.01030.04332.4733-0.494321.1738
34.804-0.5475-2.85091.8086-0.26735.14550.0289-0.170.0395-0.01530.033-0.09370.01570.1823-0.06180.057-0.01430.00290.02520.00560.0614.14295.086519.0764
42.01860.0520.65195.34380.46535.1304-0.05810.0243-0.0004-0.49150.0646-0.448-0.23920.1508-0.00650.0816-0.01310.0750.0102-0.00730.076311.2438-5.099810.7713
520.24283.243-6.74523.0103-0.65257.84610.1523-0.71640.39920.1147-0.0619-0.1348-0.18190.4422-0.09040.0708-0.0147-0.00660.0325-0.00790.07645.798-1.514826.1124
61.5595-0.1598-0.54511.2909-1.37834.28980.04890.15420.0431-0.0573-0.0006-0.01660.0857-0.0377-0.04820.05690.00460.0050.05280.00180.0549-0.842-5.814817.0004
72.2204-0.20680.60910.83660.41690.9603-0.0201-0.03-0.04410.05860.004-0.00050.0842-0.04770.01620.06030.00940.00660.03720.00660.0566-2.3578-13.341520.7428
81.57062.0871-0.4464.26270.86010.82240.0914-0.208-0.0692-0.0524-0.1435-0.17040.0086-0.01980.05210.0902-0.01020.03010.0803-0.02990.10885.7459-13.765614.2571
92.64212.6803-0.39524.5757-0.88890.9904-0.0432-0.1372-0.2054-0.0599-0.0352-0.38930.06980.17670.07850.04260.01910.00710.0787-0.0010.100610.2544-15.753118.5308
103.23030.44250.21190.63070.70090.56530.0263-0.0499-0.04370.1022-0.03610.01450.07-0.02780.00990.07020.00210.00390.04480.0020.0691-4.1744-18.487520.4737
113.8785-1.0889-0.88554.36524.25354.26940.0117-0.00730.20470.07410.213-0.41190.01650.2265-0.22480.0654-0.0012-0.02540.08640.01550.11358.2029-8.823927.5131
127.1324-0.6783-5.41840.950.52016.3077-0.0574-0.5465-0.10810.0675-0.11710.0902-0.00490.23190.17450.06250.01750.00760.0962-0.01060.0316-7.8537-8.885437.793
134.14732.1718-3.93321.0119-2.43056.86870.1015-0.08340.29160.0310.0090.1494-0.1290.0854-0.11050.06510.00970.02210.04990.00030.1036-10.96271.287326.3127
141.6034-0.4792-1.21062.8411-0.52161.03620.01410.03080.0076-0.01930.0027-0.03910.0064-0.0427-0.01680.0479-0.00350.00440.06340.00490.069-19.2965-7.836330.5282
153.1391-3.19891.481511.0961-6.09723.40670.18520.09670.0229-0.0845-0.13040.1754-0.0252-0.0156-0.05480.09040.04050.02580.09450.00320.0567-21.1952-1.660325.4588
164.9972-3.5922.63723.0446-0.20044.5465-0.0242-0.2980.1510.14720.2008-0.1752-0.0534-0.3366-0.17660.10020.04070.02960.11360.04280.075-15.41512.107616.1739
17-0.0464-0.0983-0.95890.08550.21078.2343-0.0046-0.01160.01760.0157-0.02330.0819-0.0863-0.08440.02780.0682-0.0020.00730.0814-0.01030.0889-8.2733-4.511824.2992
181.2526-0.2888-0.64471.02830.39161.56-0.00960.02630.05980.03750.00330.10620.02020.02990.00640.0473-0.00450.01510.03410.00160.0557-11.9074-6.724627.4675
191.6649-0.08530.36961.5542-1.27312.3753-0.1090.031-0.04890.07910.24510.1219-0.0681-0.2818-0.13610.0493-0.00440.02130.07730.01580.0389-17.8405-7.085622.0488
2032.4633-0.7705-16.5455.0013-6.615112.44-1.6057-1.5181-1.5728-0.43970.2449-0.06081.09660.60941.36080.20660.10010.10940.05930.08030.1232-5.8753-18.913630.9288
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A982 - 988
2X-RAY DIFFRACTION2A989 - 1004
3X-RAY DIFFRACTION3A1005 - 1012
4X-RAY DIFFRACTION4A1013 - 1027
5X-RAY DIFFRACTION5A1028 - 1033
6X-RAY DIFFRACTION6A1034 - 1048
7X-RAY DIFFRACTION7A1049 - 1060
8X-RAY DIFFRACTION8A1061 - 1066
9X-RAY DIFFRACTION9A1067 - 1074
10X-RAY DIFFRACTION10A1075 - 1085
11X-RAY DIFFRACTION11A1086 - 1093
12X-RAY DIFFRACTION12A1094 - 1101
13X-RAY DIFFRACTION13A1102 - 1114
14X-RAY DIFFRACTION14A1115 - 1122
15X-RAY DIFFRACTION15A1123 - 1129
16X-RAY DIFFRACTION16A1130 - 1136
17X-RAY DIFFRACTION17A1137 - 1144
18X-RAY DIFFRACTION18A1145 - 1159
19X-RAY DIFFRACTION19A1160 - 1172
20X-RAY DIFFRACTION20A1173 - 1179

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