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Yorodumi- PDB-3o8c: Visualizing ATP-dependent RNA Translocation by the NS3 Helicase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o8c | ||||||
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Title | Visualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCV | ||||||
Components |
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Keywords | HYDROLASE/RNA / helicase / NTPase / HCV / RNA / translocation / protease/NTPase/helicase / HYDROLASE-RNA complex | ||||||
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 / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / 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 subtype 1b | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 | 3o8c.cif.gz | 272.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o8c.ent.gz | 215 KB | Display | PDB format |
PDBx/mmJSON format | 3o8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/3o8c ftp://data.pdbj.org/pub/pdb/validation_reports/o8/3o8c | HTTPS FTP |
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-Related structure data
Related structure data | 3o8bSC 3o8dC 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
#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 #2: RNA chain | | Mass: 1870.933 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This oligonucleotide was created with an automated RNA/DNA synthesizer using phosphoramidite chemistry. #3: Chemical | #4: Chemical | #5: 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: 2.51 Å3/Da / Density % sol: 51.07 % | ||||||||||||||||||||||||||||||||||||
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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 | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-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: Aug 18, 2008 |
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→50 Å / Num. all: 97089 / Num. obs: 97089 / % possible obs: 99 % / Observed criterion σ(F): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 3.1 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3O8B Resolution: 2→47.219 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.26 / σ(F): 0 / Phase error: 23.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.109 Å2 / ksol: 0.338 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→47.219 Å
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Refine LS restraints |
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LS refinement shell |
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