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- PDB-5eqr: Crystal structure of a genotype 1a/3a chimeric HCV NS3/4A proteas... -

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Basic information

Entry
Database: PDB / ID: 5eqr
TitleCrystal structure of a genotype 1a/3a chimeric HCV NS3/4A protease in complex with danoprevir
ComponentsNS3 protease
KeywordsHYDROLASE/HYDROLASE Inhibitor / danoprevir / drug resistance / HCV protease inhibitor / genotype 3 / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex
Function / homology
Function and homology information


transformation of host cell by virus / host cell membrane / serine-type peptidase activity / virion component / symbiont entry into host cell / virion attachment to host cell / proteolysis / membrane / metal ion binding
Similarity search - Function
Thrombin, subunit H - #120 / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-TSV / NS3 protease / NS3 protease
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 Å
AuthorsSoumana, D. / Yilmaz, N.K. / Ali, A. / Prachanronarong, K.L. / Schiffer, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI085051 United States
Citation
Journal: J.Am.Chem.Soc. / Year: 2016
Title: Molecular and Dynamic Mechanism Underlying Drug Resistance in Genotype 3 Hepatitis C NS3/4A Protease.
Authors: Soumana, D.I. / Kurt Yilmaz, N. / Ali, A. / Prachanronarong, K.L. / Schiffer, C.A.
#1: Journal: 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
DepositionNov 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8664
Polymers20,9751
Non-polymers8913
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.970, 58.494, 59.985
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 NS3 protease


Mass: 20974.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Plasmid: pET28-a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: C1KIK8, UniProt: A0A0B4WYC6*PLUS
#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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 14041 / % possible obs: 96.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.09 / Χ2: 1.071 / Net I/av σ(I): 15.779 / Net I/σ(I): 7.7 / Num. measured all: 60292
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.96-2.033.70.35512011.16385.2
2.03-2.114.40.30713701.10896.5
2.11-2.214.40.25213771.06697
2.21-2.324.40.19313911.0997.3
2.32-2.474.40.16614011.10797.8
2.47-2.664.40.13614100.99497.8
2.66-2.934.40.09614191.08998.7
2.93-3.354.40.06814471.03199.2
3.35-4.224.30.05114731.06199.4
4.22-504.10.05315521.03698.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.28 Å26.69 Å
Translation2.28 Å26.69 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASER2.5.5phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→26.328 Å / FOM work R set: 0.8627 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2004 1338 9.97 %Random
Rwork0.1648 12085 --
obs0.1684 13423 92.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.06 Å2 / Biso mean: 24.97 Å2 / Biso min: 7.74 Å2
Refinement stepCycle: final / Resolution: 1.96→26.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 101 121 1661
Biso mean--25.05 28.24 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121552
X-RAY DIFFRACTIONf_angle_d1.3362116
X-RAY DIFFRACTIONf_chiral_restr0.053243
X-RAY DIFFRACTIONf_plane_restr0.007266
X-RAY DIFFRACTIONf_dihedral_angle_d24.836604
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9577-2.02760.2811090.193296076
2.0276-2.10880.26591260.1834116491
2.1088-2.20470.22591310.1678117192
2.2047-2.32090.20181250.1728120593
2.3209-2.46620.24561240.1661120593
2.4662-2.65640.21011520.1782120394
2.6564-2.92340.23451350.1788121894
2.9234-3.34580.17961440.1644127497
3.3458-4.21250.16821420.1392130699
4.21250.16491500.1617137999
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)
11.0699-0.524-0.82843.3991.8592.9839-0.04830.0663-0.074-0.29440.1013-0.21040.31460.01910.06820.2443-0.03080.04840.12170.01550.13515.5463-11.1628.5357
22.8209-1.2902-1.37693.04880.91022.86180.0515-0.01060.0224-0.1404-0.0317-0.1755-0.06250.119-0.04540.1198-0.03950.02540.1019-0.00210.15257.4984-0.051217.5651
30.7315-0.025-0.20151.19720.14010.62440.03580.0263-0.00170.0519-0.0093-0.04670.03890.0422-0.01390.07810.0082-0.00060.1043-0.00360.10421.314-12.336419.4067
41.0517-0.0731-0.37710.6099-0.5510.98680.0767-0.08910.15870.0875-0.0311-0.0087-0.10520.0631-0.06110.1598-0.01250.01630.1375-0.01940.1557-10.2438-2.543830.6943
50.5809-0.4119-0.2680.336-0.16782.67580.00320.04190.11660.08960.04340.0339-0.2286-0.2081-0.04970.09780.01890.02510.18440.00620.1729-19.3091-1.909423.4234
60.9098-0.0211-0.8651.05740.07391.7541-0.0120.03560.02760.05830.0130.04730.0538-0.1344-0.03290.1165-0.01040.01210.11790.00720.1399-12.4197-8.077825.1365
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 982 through 999 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1000 through 1032 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1033 through 1091 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1092 through 1118 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1119 through 1134 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1135 through 1179 )A0

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