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- PDB-2k1q: NMR structure of hepatitis c virus ns3 serine protease complexed ... -

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Basic information

Entry
Database: PDB / ID: 2k1q
TitleNMR structure of hepatitis c virus ns3 serine protease complexed with the non-covalently bound phenethylamide inhibitor
Components
  • NS3 PROTEASE
  • PHENETHYLAMIDE
KeywordsVIRAL PROTEIN / SERINE PROTEASE / NS3 / HEPATITIS C VIRUS / NON COVALENT INHIBITOR / Envelope protein / Helicase / Hydrolase / Nucleotide-binding / RNA replication / Transmembrane
Function / homology
Function and homology information


host cell lipid droplet / transformation of host cell by virus / host cell mitochondrion / 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 ...host cell lipid droplet / transformation of host cell by virus / host cell mitochondrion / 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 / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / induction by virus of host autophagy / ribonucleoprotein complex / symbiont entry into host cell / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / 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 / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / 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
Biological speciesHepatitis C virus
MethodSOLUTION NMR / simulated annealing
AuthorsEliseo, T. / Gallo, M. / Pennestri, M. / Bazzo, R. / Cicero, D.O.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Binding of a noncovalent inhibitor exploiting the S' region stabilizes the hepatitis C virus NS3 protease conformation in the absence of cofactor.
Authors: Gallo, M. / Pennestri, M. / Bottomley, M.J. / Barbato, G. / Eliseo, T. / Paci, M. / Narjes, F. / De Francesco, R. / Summa, V. / Koch, U. / Bazzo, R. / Cicero, D.O.
History
DepositionMar 13, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NS3 PROTEASE
B: PHENETHYLAMIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3633
Polymers20,2982
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein NS3 PROTEASE


Mass: 19634.529 Da / Num. of mol.: 1 / Fragment: residues 1048-1206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Strain: 1B / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P90191
#2: Protein/peptide PHENETHYLAMIDE


Mass: 663.107 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D HNCO
1223D HNCA
1323D HN(CO)CA
1423D CBCA(CO)NH
1523D (H)CCH-TOCSY
1623D (H)CCH-COSY
1723D 1H-13C NOESY
1813D 1H-15N NOESY
1913D 1H-15N TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM [U-100% 15N] NS3 PROTEASE, 50 uM ZINC ION, 0.9 mM phenetylamide, 50 mM sodium phosphate, 0.3 % [U-100% 2H] beta-octilglucoside, 100 mM sodium chloride, 1 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
20.6 mM [U-100% 13C; U-100% 15N] NS3 PROTEASE, 50 uM ZINC ION, 0.6 mM phenetylamide, 50 % sodium phosphate, 0.3 mM [U-100% 2H] beta-octilglucoside, 100 mM sodium chloride, 1 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMNS3 PROTEASE[U-100% 15N]1
50 uMZINC ION1
0.9 mMphenetylamide1
50 mMsodium phosphate1
0.3 %beta-octilglucoside[U-100% 2H]1
100 mMsodium chloride1
1 mMDTT1
0.6 mMNS3 PROTEASE[U-100% 13C; U-100% 15N]2
50 uMZINC ION2
0.6 mMphenetylamide2
50 %sodium phosphate2
0.3 mMbeta-octilglucoside[U-100% 2H]2
100 mMsodium chloride2
1 mMDTT2
Sample conditionsIonic strength: 0.15 / pH: 6.8 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE5003
Bruker AvanceBrukerAVANCE4004

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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