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Yorodumi- PDB-1nhv: Hepatitis C virus RNA polymerase in complex with non-nucleoside a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nhv | ||||||
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Title | Hepatitis C virus RNA polymerase in complex with non-nucleoside analogue inhibitor | ||||||
Components | HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASE | ||||||
Keywords | TRANSFERASE / HEPATITIS C / RNA POLYMERASE / ENZYME INHIBITION | ||||||
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 / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Hepatitis C virus subtype 1b | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Wang, M. / Ng, K.K.S. / Cherney, M.M. / Chan, L. / Yannopoulos, C.G. / Bedard, J. / Morin, N. / Nguyen-Ba, N. / Alaoui-Ismaili, M.H. / Bethell, R.C. / James, M.N.G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Non-Nucleoside Analogue Inhibitors Bind to an Allosteric Site on HCV NS5B Polymerase: Crystal Structures and Mechanism of Inhibition Authors: Wang, M. / Ng, K.K.S. / Cherney, M.M. / Chan, L. / Yannopoulos, C.G. / Bedard, J. / Morin, N. / Nguyen-Ba, N. / Alaoui-Ismaili, M.H. / Bethell, R.C. / James, M.N.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nhv.cif.gz | 225.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nhv.ent.gz | 180.1 KB | Display | PDB format |
PDBx/mmJSON format | 1nhv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/1nhv ftp://data.pdbj.org/pub/pdb/validation_reports/nh/1nhv | HTTPS FTP |
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-Related structure data
Related structure data | 1nhuC 1c2pS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 64261.613 Da / Num. of mol.: 2 / Fragment: residues 2420-2989 of polyprotein Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus subtype 1b / Genus: Hepacivirus / Species: Hepatitis C virus / Strain: subtype 1b / Variant: type 1b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P26663, RNA-directed RNA polymerase #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 47.8 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18% (w/v) PEG 4000, 0.3 M NaCl, 0.1 M sodium acetate buffer (pH = 5.0), 5 mM 2-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 7, 2001 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→40 Å / Num. all: 25058 / Num. obs: 25058 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 51.8 Å2 / Rsym value: 0.11 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2263 / Rsym value: 0.353 / % possible all: 86.2 |
Reflection | *PLUS Highest resolution: 2.9 Å / % possible obs: 95.2 % / Num. measured all: 91256 / Rmerge(I) obs: 0.11 |
Reflection shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 86.2 % / Rmerge(I) obs: 0.353 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C2P Resolution: 2.9→39.74 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2488343.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 23.4673 Å2 / ksol: 0.351953 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.4 Å2
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Refine analyze | Luzzati coordinate error free: 0.47 Å / Luzzati sigma a free: 0.53 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→39.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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