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Yorodumi- PDB-3o8b: Visualizing ATP-dependent RNA Translocation by the NS3 Helicase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o8b | ||||||
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Title | Visualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCV | ||||||
Components | HCV NS3 protease/helicase | ||||||
Keywords | HYDROLASE / helicase / NTPase / HCV / RNA / translocation / protein-RNA complex / protease/NTPase/helicase | ||||||
Function / homology | Function and homology information 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 / ribonucleoside triphosphate phosphatase activity / lipid droplet / : ...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 / ribonucleoside triphosphate phosphatase activity / lipid droplet / : / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / induction by virus of host autophagy / ribonucleoprotein complex / 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 / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Hepatitis C virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Appleby, T.C. / Somoza, J.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Visualizing ATP-Dependent RNA Translocation by the NS3 Helicase from HCV. Authors: Appleby, T.C. / Anderson, R. / Fedorova, O. / Pyle, A.M. / Wang, R. / Liu, X. / Brendza, K.M. / Somoza, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o8b.cif.gz | 271.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o8b.ent.gz | 215.1 KB | Display | PDB format |
PDBx/mmJSON format | 3o8b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/3o8b ftp://data.pdbj.org/pub/pdb/validation_reports/o8/3o8b | HTTPS FTP |
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-Related structure data
Related structure data | 3o8cC 3o8dC 3o8rC 1cu1S 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: 70869.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q99AU2, hepacivirin, nucleoside-triphosphate phosphatase, RNA helicase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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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: 2.52 Å3/Da / Density % sol: 51.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% (w/v) PEG 3350, 160 mM LiSO4, 80 mM Bis-Tris, 10% (v/v) glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2007 |
Radiation | Monochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 102574 / Num. obs: 102574 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rsym value: 0.067 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 1.95→2.01 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.486 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1CU1 Resolution: 1.95→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å
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