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Yorodumi- PDB-1os5: Crystal structure of HCV NS5B RNA polymerase complexed with a nov... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1os5 | ||||||
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Title | Crystal structure of HCV NS5B RNA polymerase complexed with a novel non-competitive inhibitor. | ||||||
Components | Hepatitis C virus NS5B RNA polymerase | ||||||
Keywords | TRANSFERASE / ENZYME-INHIBITOR COMPLEX | ||||||
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 / structural molecule activity / host cell plasma membrane / virion membrane / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Hepatitis C virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Love, R.A. / Parge, H.E. / Yu, X. / Hickey, M.J. / Diehl, W. / Gao, J. / Wriggers, H. / Ekker, A. / Wang, L. / Thomson, J.A. ...Love, R.A. / Parge, H.E. / Yu, X. / Hickey, M.J. / Diehl, W. / Gao, J. / Wriggers, H. / Ekker, A. / Wang, L. / Thomson, J.A. / Dragovich, P.S. / Fuhrman, S.A. | ||||||
Citation | Journal: J.Virol. / Year: 2003 Title: Crystallographic identification of a noncompetitive inhibitor binding site on the hepatitis C virus NS5B RNA polymerase enzyme. Authors: Love, R.A. / Parge, H.E. / Yu, X. / Hickey, M.J. / Diehl, W. / Gao, J. / Wriggers, H. / Ekker, A. / Wang, L. / Thomson, J.A. / Dragovich, P.S. / Fuhrman, S.A. #1: Journal: Patent / Year: 2002 Title: Hepatitis C Virus (HCV) NS5B RNA Polymerase and Mutants Thereof. Authors: Love, R.A. / Parge, H.E. / Hickey, M.J. / Yu, X. / Fuhrman, S.A. / Diehl, W. / Gao, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1os5.cif.gz | 135.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1os5.ent.gz | 105 KB | Display | PDB format |
PDBx/mmJSON format | 1os5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/1os5 ftp://data.pdbj.org/pub/pdb/validation_reports/os/1os5 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 64162.457 Da / Num. of mol.: 1 / Mutation: L47Q, F101Y, K114R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus / Genus: Hepacivirus / Strain: subtype 1b / Gene: NS5B / Production host: Escherichia coli (E. coli) / References: UniProt: P26663 |
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#2: Chemical | ChemComp-NH1 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal |
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Crystal grow |
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Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 9, 2000 |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 31863 / Num. obs: 31057 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.108 / Mean I/σ(I) obs: 10 / Num. unique all: 2500 / % possible all: 72 |
Reflection shell | *PLUS % possible obs: 72 % / Mean I/σ(I) obs: 15 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NS5B polymerase with single mutation at K106Q or K114R. Resolution: 2.2→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 18 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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