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- PDB-3sv8: Crystal structure of NS3/4A protease variant D168A in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3sv8
TitleCrystal structure of NS3/4A protease variant D168A in complex with Telaprevir
ComponentsNS3 protease, NS4A protein
KeywordsVIRAL PROTEIN / HYDROLASE/INHIBITOR / drug resistance / drug design / Protease inhibitors / serine protease / 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 / ribonucleoside triphosphate phosphatase activity / lipid droplet / : ...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 / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / 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 / Hepatitis C virus, Core protein, N-terminal ...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-SV6 / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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

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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)22,2994
Polymers21,4591
Non-polymers8393
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.532, 69.532, 79.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Detailsbiological unit is the same as asym.

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Components

#1: Protein NS3 protease, NS4A protein


Mass: 21459.320 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, D1168A
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 / Telaprevir


Type: peptide-like / Mass: 681.865 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H55N7O6 / Comment: antivirus, protease inhibitor*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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 / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.75 %
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 31, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 7049 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.136 / Χ2: 2.195 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.6970.56111701.0661100
2.69-2.870.44211471.2691100
2.8-2.937.10.32811751.5681100
2.93-3.087.20.27311681.8591100
3.08-3.287.20.21111522.0911100
3.28-3.537.30.16611732.435199.9
3.53-3.887.20.14411653.5141100
3.88-4.447.40.09611743.1521100
4.44-5.597.40.07411762.4131100
5.59-307.20.06311902.454198.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→21.99 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.884 / WRfactor Rfree: 0.2877 / WRfactor Rwork: 0.202 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7686 / SU B: 24.84 / SU ML: 0.27 / SU R Cruickshank DPI: 0.7302 / SU Rfree: 0.3391 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2825 332 4.7 %RANDOM
Rwork0.2053 ---
obs0.2089 7049 98.86 %-
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: 100.07 Å2 / Biso mean: 52.5702 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.5→21.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1388 0 56 44 1488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211471
X-RAY DIFFRACTIONr_bond_other_d0.0010.02978
X-RAY DIFFRACTIONr_angle_refined_deg1.35222006
X-RAY DIFFRACTIONr_angle_other_deg1.06532385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.255192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3321.70247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.00715211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0971513
X-RAY DIFFRACTIONr_chiral_restr0.0730.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211635
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
X-RAY DIFFRACTIONr_mcbond_it0.4331.5959
X-RAY DIFFRACTIONr_mcbond_other0.0671.5398
X-RAY DIFFRACTIONr_mcangle_it0.80821541
X-RAY DIFFRACTIONr_scbond_it1.2513512
X-RAY DIFFRACTIONr_scangle_it1.6094.5462
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 18 -
Rwork0.265 480 -
all-498 -
obs--97.46 %
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)
13.08161.6245-1.37082.76892.87057.3667-0.1177-0.18310.034-0.0754-0.08640.15370.0610.03540.20410.1543-0.0453-0.0430.46150.10430.5266-20.03227.2688-1.4529
23.99850.1455-3.00555.3799-1.46142.7775-0.11860.101-0.0462-0.41460.07960.5176-0.0115-0.02080.0390.381-0.036-0.1010.30550.01630.261-22.052425.4189-6.7107
32.13343.8037-0.25077.2527-0.55210.0530.354-0.2605-0.1550.5965-0.28560.2168-0.0376-0.0088-0.06840.53240.01570.04750.37830.04550.613-26.45745.79741.0428
47.40222.2379-1.66361.5903-2.98037.11860.05080.3903-0.0375-0.120.17260.12320.2835-0.0566-0.22350.2465-0.0045-0.07140.3078-0.05220.5763-23.69189.3621-8.5214
54.7019-1.56372.44688.24751.56792.0221-0.6146-0.6338-0.02770.70570.43280.1298-0.2167-0.30410.18170.2940.0311-0.01480.3121-0.03510.4992-18.130510.97631.1088
63.4877-0.08880.84443.55861.92561.272-0.1922-0.1125-0.1836-0.01870.08170.294-0.0360.01540.11050.36160.025-0.05870.31690.03810.3356-12.408413.7983-4.5036
72.7111-0.02350.35865.4747-0.9850.49050.1745-0.0229-0.6527-0.0175-0.06570.28780.294-0.1005-0.10880.3093-0.0275-0.01370.28630.00270.2867-8.10999.2906-0.9697
89.13532.5182-0.05168.10262.68640.98930.3445-0.2962-0.44770.3635-0.44550.17090.1372-0.12950.1010.3994-0.0179-0.04190.282-0.00370.3873-14.92332.0167-3.4272
96.15771.94552.05773.32350.44872.6803-0.00530.1003-0.4182-0.52880.1107-0.0120.1821-0.1731-0.10540.41160.0097-0.08220.2699-0.00590.3596-9.00283.4623-7.5028
1015.69543.256313.66665.891-2.307218.73240.46040.6977-0.4631-0.17880.3222-0.13760.27730.0666-0.78260.21370.08010.01870.3371-0.02250.2365-8.04027.8025-5.7784
1116.066510.8176-4.090116.94.56126.6236-0.37150.8860.0837-0.67840.15080.5846-0.2924-0.52430.22070.32710.0174-0.10530.44420.02980.5678-17.125612.8887-14.2148
124.16582.2393-0.13224.3102-0.90810.88020.13050.16530.0729-0.3450.0384-0.012-0.18620.1804-0.16890.33380.01450.00440.35530.01730.2339-4.790727.8681-7.7451
1342.7846-2.52718.362310.69782.94972.7588-0.3843-0.5512-1.2431.45870.45280.49010.38360.0118-0.06850.42210.03420.08720.30270.03060.2635-17.994523.44262.4857
149.88432.19186.08422.26660.25254.7203-0.13510.22470.45170.33690.0157-0.1199-0.23990.1570.11940.2587-0.0352-0.06280.3205-0.00330.3023-5.666530.59880.6379
151.22421.54141.00210.1495-0.04422.4041-0.12060.2192-0.09480.3162-0.01010.0813-0.2566-0.03650.13070.3221-0.01570.03060.336-0.01550.2867-1.486628.45044.9628
1610.8450.00286.91893.29767.172220.0062-0.242-0.1641-0.32680.02040.01370.2003-0.1248-0.09510.22840.32650.02510.02070.3860.02020.382-13.527424.145810.9119
170.2650.4372-0.438112.0746-8.04065.68380.1474-0.02490.0355-0.1712-0.0853-0.2257-0.0393-0.0819-0.06210.2954-0.0041-0.01460.3390.0030.2885-9.547823.9326-3.6138
185.1151-0.91055.09352.1291-0.30655.25690.14070.0236-0.0740.0253-0.06050.02910.13630.0089-0.08020.2512-0.01520.01340.2611-0.00870.2389-5.194921.03581.0954
193.3656-0.9072-1.10232.3904-0.54210.69320.0569-0.49340.11770.30570.0153-0.0446-0.1660.2248-0.07220.3024-0.07610.01640.3542-0.03960.2722-3.690822.86076.5441
2012.97390.7355-1.37432.57040.48630.2763-0.6830.72580.424-0.8240.70750.089-0.12860.0421-0.02450.4372-0.10010.01260.3967-0.02560.2990.787814.0184-10.1857
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A989 - 997
2X-RAY DIFFRACTION2A998 - 1008
3X-RAY DIFFRACTION3A1009 - 1021
4X-RAY DIFFRACTION4A1022 - 1032
5X-RAY DIFFRACTION5A1033 - 1040
6X-RAY DIFFRACTION6A1041 - 1051
7X-RAY DIFFRACTION7A1052 - 1060
8X-RAY DIFFRACTION8A1061 - 1066
9X-RAY DIFFRACTION9A1067 - 1080
10X-RAY DIFFRACTION10A1081 - 1086
11X-RAY DIFFRACTION11A1087 - 1093
12X-RAY DIFFRACTION12A1094 - 1106
13X-RAY DIFFRACTION13A1107 - 1112
14X-RAY DIFFRACTION14A1113 - 1118
15X-RAY DIFFRACTION15A1119 - 1129
16X-RAY DIFFRACTION16A1130 - 1136
17X-RAY DIFFRACTION17A1137 - 1148
18X-RAY DIFFRACTION18A1149 - 1159
19X-RAY DIFFRACTION19A1160 - 1172
20X-RAY DIFFRACTION20A1173 - 1179

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