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Yorodumi- PDB-3o8d: Visualizing ATP-dependent RNA Translocation by the NS3 Helicase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o8d | ||||||
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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 / ADP / beryllium trifluoride / 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 / protein complex oligomerization ...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 perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / induction by virus of host autophagy / serine-type endopeptidase activity / cysteine-type endopeptidase activity / 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 / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / zinc ion binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Hepatitis C virus subtype 1b | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 | 3o8d.cif.gz | 273 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o8d.ent.gz | 214.3 KB | Display | PDB format |
PDBx/mmJSON format | 3o8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3o8d_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3o8d_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3o8d_validation.xml.gz | 53.5 KB | Display | |
Data in CIF | 3o8d_validation.cif.gz | 78.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/3o8d ftp://data.pdbj.org/pub/pdb/validation_reports/o8/3o8d | HTTPS FTP |
-Related structure data
Related structure data | 3o8bSC 3o8cC 3o8rC 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 70869.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus subtype 1b / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q99AU2, hepacivirin, nucleoside-triphosphate phosphatase, RNA helicase |
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-Non-polymers , 5 types, 846 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 51.26 % |
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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: Feb 17, 2009 |
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: 2.05→50 Å / Num. obs: 90501 / % possible obs: 99.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 3 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3O8B Resolution: 2.05→47.024 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.27 / σ(F): 0 / Phase error: 23.94 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.792 Å2 / ksol: 0.349 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→47.024 Å
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Refine LS restraints |
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LS refinement shell |
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