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- PDB-1bt7: THE SOLUTION NMR STRUCTURE OF THE N-TERMINAL PROTEASE DOMAIN OF T... -

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Entry
Database: PDB / ID: 1bt7
TitleTHE SOLUTION NMR STRUCTURE OF THE N-TERMINAL PROTEASE DOMAIN OF THE HEPATITIS C VIRUS (HCV) NS3-PROTEIN, FROM BK STRAIN, 20 STRUCTURES
ComponentsNS3 SERINE PROTEASE
KeywordsHYDROLASE / VIRAL NON-STRUCTURAL PROTEIN / SERINE PROTEASE
Function / homology
Function and homology information


hepacivirin / 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 / SH3 domain binding / : ...hepacivirin / 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 / SH3 domain binding / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / RNA helicase / induction by virus of host autophagy / ribonucleoprotein complex / RNA-directed RNA polymerase / 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 / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
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 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
Biological speciesHepatitis C virus
MethodSOLUTION NMR / DG-SA HYBRID
AuthorsBarbato, G. / Cicero, D.O. / Nardi, M.C. / Steinkuhler, C. / Cortese, R. / De Francesco, R. / Bazzo, R.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: The solution structure of the N-terminal proteinase domain of the hepatitis C virus (HCV) NS3 protein provides new insights into its activation and catalytic mechanism.
Authors: Barbato, G. / Cicero, D.O. / Nardi, M.C. / Steinkuhler, C. / Cortese, R. / De Francesco, R. / Bazzo, R.
#1: Journal: Protein Sci. / Year: 1998
Title: Complex of Ns3 Protease and Ns4A Peptide of Bk Strain Hepatitis C Virus: A 2.2 A Resolution Structure in a Hexagonal Crystal Form
Authors: Yan, Y. / Li, Y. / Munshi, S. / Sardana, V. / Cole, J.L. / Sardana, M. / Steinkuehler, C. / Tomei, L. / De Francesco, R. / Kuo, L.C. / Chen, Z.
#2: Journal: J.Biol.Chem. / Year: 1998
Title: The Metal Binding Site of the Hepatitis C Virus Ns3 Protease. A Spectroscopic Investigation
Authors: Urbani, A. / Bazzo, R. / Nardi, M.C. / Cicero, D.O. / De Francesco, R. / Steinkuhler, C. / Barbato, G.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Erratum. Crystal Structure of the Hepatitis C Virus Ns3 Protease Domain Complexed with a Synthetic Ns4A Cofactor Peptide
Authors: Kim, J.L. / Morgenstern, K.A. / Lin, C. / Fox, T. / Dwyer, M.D. / Landro, J.A. / Chambers, S.P. / Markland, W. / Lepre, C.A. / O'Malley, E.T. / Harbeson, S.L. / Rice, C.M. / Murcko, M.A. / ...Authors: Kim, J.L. / Morgenstern, K.A. / Lin, C. / Fox, T. / Dwyer, M.D. / Landro, J.A. / Chambers, S.P. / Markland, W. / Lepre, C.A. / O'Malley, E.T. / Harbeson, S.L. / Rice, C.M. / Murcko, M.A. / Caron, P.R. / Thomson, J.A.
#4: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Crystal Structure of the Hepatitis C Virus Ns3 Protease Domain Complexed with a Synthetic Ns4A Cofactor Peptide
Authors: Kim, J.L. / Morgenstern, K.A. / Lin, C. / Fox, T. / Dwyer, M.D. / Landro, J.A. / Chambers, S.P. / Markland, W. / Lepre, C.A. / O'Malley, E.T. / Harbeson, S.L. / Rice, C.M. / Murcko, M.A. / ...Authors: Kim, J.L. / Morgenstern, K.A. / Lin, C. / Fox, T. / Dwyer, M.D. / Landro, J.A. / Chambers, S.P. / Markland, W. / Lepre, C.A. / O'Malley, E.T. / Harbeson, S.L. / Rice, C.M. / Murcko, M.A. / Caron, P.R. / Thomson, J.A.
#5: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: The Crystal Structure of Hepatitis C Virus Ns3 Proteinase Reveals a Trypsin-Like Fold and a Structural Zinc Binding Site
Authors: Love, R.A. / Parge, H.E. / Wickersham, J.A. / Hostomsky, Z. / Habuka, N. / Moomaw, E.W. / Adachi, T. / Hostomska, Z.
History
DepositionSep 1, 1998Processing site: BNL
Revision 1.0Jun 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name / _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

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: NS3 SERINE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7002
Polymers19,6351
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 / 60LEAST RESTRAINT VIOLATIONS/MINIMUM ENERGY
Representative

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Components

#1: Protein NS3 SERINE PROTEASE


Mass: 19634.529 Da / Num. of mol.: 1 / Mutation: INS(R180-ASKKKK)
Source method: isolated from a genetically manipulated source
Details: COMPOUND ENGINEERED ADDING A SOLUBILISING TAIL AT THE C-TERMINUS
Source: (gene. exp.) Hepatitis C virus / Genus: Hepacivirus / Strain: BK / Plasmid: PT7.7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P26663
#2: 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 detailsText: THE STRUCTURE WAS DETERMINED USING N15, N15/C13, N15/C13/2H, AND 15N SELECTIVELY LABELED SAMPLES, WITH TRIPLE RESONANCE EXPERIMENTS

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Sample preparation

DetailsContents: 90% H2O/5% D2O/ 5% GLYCEROL-D
Sample conditionspH: 6.3 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Varian DMXVarianDMX6002
Varian UNITYPLUSVarianUNITYPLUS8003
Varian DMXVarianDMX8004

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
NMRPipestructure solution
NMRViewstructure solution
RefinementMethod: DG-SA HYBRID / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. R.M.S. DEVIATIONS FROM EXPERIMENTAL RESTRAINTS: DISTANCE (ANGSTROMS) : 0.076 +/- 0.003 DIHEDRAL (DEGREES) : 1.331 +/- 0.148 ...Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. R.M.S. DEVIATIONS FROM EXPERIMENTAL RESTRAINTS: DISTANCE (ANGSTROMS) : 0.076 +/- 0.003 DIHEDRAL (DEGREES) : 1.331 +/- 0.148 IDEALIZED GEOMETRY BONDS (ANGSTROMS): 0.005 +/- 0.0006 ANGLES (DEGREES) : 0.761 +/- 0.032 IMPROPERS (DEGREES) : 0.543 +/- 0.017
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATIONS/MINIMUM ENERGY
Conformers calculated total number: 60 / Conformers submitted total number: 20

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