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Yorodumi- PDB-1bt7: THE SOLUTION NMR STRUCTURE OF THE N-TERMINAL PROTEASE DOMAIN OF T... -
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-Basic information
Entry | Database: PDB / ID: 1bt7 | ||||||
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Title | THE SOLUTION NMR STRUCTURE OF THE N-TERMINAL PROTEASE DOMAIN OF THE HEPATITIS C VIRUS (HCV) NS3-PROTEIN, FROM BK STRAIN, 20 STRUCTURES | ||||||
Components | NS3 SERINE PROTEASE | ||||||
Keywords | HYDROLASE / 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 / nucleoside-triphosphate phosphatase ...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 / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / 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 / RNA helicase / ribonucleoprotein complex / induction by virus of host autophagy / serine-type endopeptidase activity / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / 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 / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Hepatitis C virus | ||||||
Method | SOLUTION NMR / DG-SA HYBRID | ||||||
Authors | Barbato, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bt7.cif.gz | 967.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bt7.ent.gz | 799.5 KB | Display | PDB format |
PDBx/mmJSON format | 1bt7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bt7_validation.pdf.gz | 363.5 KB | Display | wwPDB validaton report |
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Full document | 1bt7_full_validation.pdf.gz | 579.9 KB | Display | |
Data in XML | 1bt7_validation.xml.gz | 80 KB | Display | |
Data in CIF | 1bt7_validation.cif.gz | 105.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/1bt7 ftp://data.pdbj.org/pub/pdb/validation_reports/bt/1bt7 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR details | Text: THE STRUCTURE WAS DETERMINED USING N15, N15/C13, N15/C13/2H, AND 15N SELECTIVELY LABELED SAMPLES, WITH TRIPLE RESONANCE EXPERIMENTS |
-Sample preparation
Details | Contents: 90% H2O/5% D2O/ 5% GLYCEROL-D |
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Sample conditions | pH: 6.3 / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
Software |
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NMR software |
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Refinement | Method: 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 ensemble | Conformer selection criteria: LEAST RESTRAINT VIOLATIONS/MINIMUM ENERGY Conformers calculated total number: 60 / Conformers submitted total number: 20 |