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- PDB-3m5l: Crystal structure of HCV NS3/4A protease in complex with ITMN-191 -

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Basic information

Entry
Database: PDB / ID: 3m5l
TitleCrystal structure of HCV NS3/4A protease in complex with ITMN-191
ComponentsNS3/4A
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HCV / Hepatitis C Virus / NS3 / protease / drug resistance / serine protease / chimera protein / fusion protein / 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 / 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 / lipid droplet / ribonucleoside triphosphate phosphatase activity / channel activity ...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 / lipid droplet / ribonucleoside triphosphate phosphatase activity / channel activity / monoatomic ion transmembrane transport / 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 / induction by virus of host autophagy / ribonucleoprotein complex / 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 / host cell nucleus / virion attachment to host cell / apoptotic process / 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 / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / 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 NS2, C-terminal domain / 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, 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 NS2, C-terminal domain / 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 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 zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / Hepatitis C virus, Non-structural protein NS2 / : / NS3 RNA helicase, C-terminal helical domain / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus non-structural 5a protein membrane anchor / 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 / Hepacivirus/Pegivirus NS3 protease domain profile. / Hepatitis C virus NS3 protease / 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-TSV / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus subtype 1a
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsSchiffer, C.A. / Romano, K.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Drug resistance against HCV NS3/4A inhibitors is defined by the balance of substrate recognition versus inhibitor binding.
Authors: Romano, K.P. / Ali, A. / Royer, W.E. / Schiffer, C.A.
History
DepositionMar 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Feb 21, 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 / entity / 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 / _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_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
Remark 999The 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS3/4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3794
Polymers21,4871
Non-polymers8913
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.190, 58.740, 61.120
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 NS3/4A


Mass: 21487.330 Da / Num. of mol.: 1
Fragment: NS4A (UNP residues 1678-1688), NS3 (UNP residues 1027-1657)
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
Details: The protein crystallized is a single-chain construct of protease domain of hepatitis C virus NS3/4A, with cofactor 4A covalently linked at the N-terminus.
Source: (gene. exp.) Hepatitis C virus subtype 1a / Strain: BID-V318 / Gene: NS3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8DG50, hepacivirin
#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.: 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.: 206 / 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: 2.31 Å3/Da / Density % sol: 46.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES buffer pH 6.5, 4% (w/v) ammonium sulfate, 20-26% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Nov 24, 2009
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 55461 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Rsym value: 0.046 / Net I/σ(I): 20.04
Reflection shellResolution: 1.25→1.27 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.35 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→42.35 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.14 / SU ML: 0.023 / SU R Cruickshank DPI: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16759 2816 5.1 %RANDOM
Rwork0.14952 ---
obs0.15043 52645 99.72 %-
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 mean: 16.808 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2---0.81 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.25→42.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1419 0 57 206 1682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211585
X-RAY DIFFRACTIONr_bond_other_d0.0010.021030
X-RAY DIFFRACTIONr_angle_refined_deg1.4842.0432186
X-RAY DIFFRACTIONr_angle_other_deg1.24132532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6055206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33222.91748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.96215225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3881510
X-RAY DIFFRACTIONr_chiral_restr0.0790.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211775
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02307
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0961.5992
X-RAY DIFFRACTIONr_mcbond_other0.311.5412
X-RAY DIFFRACTIONr_mcangle_it1.71221596
X-RAY DIFFRACTIONr_scbond_it2.3853593
X-RAY DIFFRACTIONr_scangle_it3.2444.5573
X-RAY DIFFRACTIONr_rigid_bond_restr0.8932615
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 197 -
Rwork0.181 3823 -
obs--99.53 %
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)
1-3.1443-0.29030.09586.2608-3.41910.8713-0.12130.07770.1380.41160.19630.3147-0.10850.0215-0.0750.23880.06510.11730.12890.05670.1151-6.1881-16.6587-4.3658
22.01881.351-1.19754.7743-2.58133.68730.02710.20910.0739-0.25710.08140.0711-0.104-0.1036-0.10840.0760.00630.0070.0577-0.01040.0422-2.10231.7459-23.6991
33.45610.9889-2.10293.1676-0.53844.14460.02570.1419-0.02240.06910.0240.0787-0.0602-0.1759-0.04970.0740.01120.00630.0378-0.00540.051-4.03155.0041-19.1815
43.92672.48730.98666.8529-0.65086.81080.098-0.06920.03590.697-0.04680.3976-0.4235-0.2019-0.05120.12140.01060.08420.02750.00440.06-10.4763-4.7529-9.5946
519.1021-3.7257-9.15772.3602-0.44729.91140.26270.46250.2395-0.18040.0120.2619-0.3445-0.4652-0.27470.07540.0136-0.02950.0437-0.00040.1245-8.2817-1.3966-25.154
61.8902-0.5357-0.21612.6968-0.39510.32190.0576-0.22310.00540.18430.04840.0520.22420.1935-0.1060.0435-0.0040.00250.0618-0.00980.0485-0.0208-5.0466-14.4738
71.216-0.0192-0.22541.1539-0.37740.69890.0106-0.0452-0.0122-0.0457-0.0150.04950.05780.00210.00440.0451-0.0080.00160.0353-0.00620.03671.4218-11.792-20.144
83.186-2.193-0.87032.79691.29681.13350.08060.1056-0.1077-0.0654-0.09810.22880.0971-0.2320.01750.0695-0.0180.00260.10180.00710.1021-10.1934-14.5908-18.8102
92.4623-0.3616-0.1540.3894-0.22251.1471-0.006-0.0063-0.0667-0.1039-0.03740.02020.06820.0270.04330.0757-0.00320.00960.0430.00280.06055.8221-19.588-21.0984
102.5904-1.26430.70953.0536-3.07853.75610.06960.0241-0.0589-0.07180.06510.337-0.0503-0.284-0.13480.0947-0.0007-0.0430.0812-0.0260.1206-6.8884-10.374-26.2913
111.8421-0.3564-0.76520.6850.34441.68920.06110.20650.2042-0.0778-0.0154-0.1403-0.0344-0.0398-0.04560.05420.00270.02240.05010.04020.089710.184-4.1983-32.6019
1211.7076-6.4202-7.99012.02243.29859.87070.1663-0.01390.94830.07640.0949-0.6664-0.19930.1649-0.26120.0716-0.02950.05140.0087-0.01530.242711.73063.5864-24.931
133.2484-1.6382-0.48644.7611.83251.88220.0214-0.02820.1071-0.00310.0758-0.0709-0.0357-0.0118-0.09720.04060.00680.02730.0822-0.00140.065620.5072-9.0991-30.412
14-0.4147-0.23351.79120.76944.19986.2260.0698-0.08130.2091-0.3734-0.0068-0.3643-0.5147-0.1408-0.0630.1643-0.05390.12170.1519-0.09110.216720.19371.5064-22.0655
153.31231.15411.3691.06292.45925.2667-0.0827-0.04720.2087-0.14710.05670.0002-0.3230.23680.02610.0649-0.0096-0.00510.06940.00030.085610.5813-1.4219-18.8093
160.69581.6208-3.423.1484-1.24474.70550.1140.16270.34640.01320.04840.0265-0.0102-0.1511-0.16240.06950.0180.05380.12470.08960.15028.9219-4.6878-34.6543
173.80991.866-0.92891.89871.29081.8713-0.0258-0.2101-0.0347-0.0027-0.0614-0.06910.0430.1270.08730.04470.0010.01010.06880.00770.051414.0342-8.8157-20.7844
182.5132-3.829-3.81635.18327.600912.8201-0.0645-0.61580.1997-0.02160.9244-0.744-0.03451.3061-0.85990.047-0.0153-0.00590.3041-0.14960.18424.6134-2.2254-16.3488
199.29195.10073.39382.81773.73295.01620.063-0.00170.0159-0.06390.0006-0.06880.14480.1932-0.06370.0820.02040.03010.0730.00380.065614.4494-11.029-25.6835
2011.92040.5194-3.99683.20350.03612.6226-0.28170.2167-0.48260.03770.01680.03850.42230.0040.26490.1839-0.00840.0310.054-0.02880.06276.4276-18.3334-31.2343
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A986 - 991
2X-RAY DIFFRACTION2A992 - 1004
3X-RAY DIFFRACTION3A1005 - 1012
4X-RAY DIFFRACTION4A1013 - 1026
5X-RAY DIFFRACTION5A1027 - 1032
6X-RAY DIFFRACTION6A1033 - 1041
7X-RAY DIFFRACTION7A1042 - 1063
8X-RAY DIFFRACTION8A1064 - 1074
9X-RAY DIFFRACTION9A1075 - 1083
10X-RAY DIFFRACTION10A1084 - 1093
11X-RAY DIFFRACTION11A1094 - 1109
12X-RAY DIFFRACTION12A1110 - 1116
13X-RAY DIFFRACTION13A1117 - 1123
14X-RAY DIFFRACTION14A1124 - 1132
15X-RAY DIFFRACTION15A1133 - 1142
16X-RAY DIFFRACTION16A1143 - 1152
17X-RAY DIFFRACTION17A1153 - 1158
18X-RAY DIFFRACTION18A1159 - 1166
19X-RAY DIFFRACTION19A1167 - 1171
20X-RAY DIFFRACTION20A1172 - 1179

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