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Yorodumi- PDB-8ohm: CRYSTAL STRUCTURE OF RNA HELICASE FROM GENOTYPE 1B HEPATITIS C VI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ohm | ||||||
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Title | CRYSTAL STRUCTURE OF RNA HELICASE FROM GENOTYPE 1B HEPATITIS C VIRUS: MECHANISM OF UNWINDING DUPLEX RNA | ||||||
Components | RNA HELICASEHelicase | ||||||
Keywords | HELICASE / RNA HELICASE / HEPATITIS C VIRUS / HCV / UNWINDING MECHANISM | ||||||
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 / RNA-directed RNA polymerase / virus-mediated perturbation of host defense response / 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 / 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 | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.3 Å | ||||||
Authors | Cho, H.S. / Ha, N.C. / Kang, L.W. / Oh, B.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: Crystal structure of RNA helicase from genotype 1b hepatitis C virus. A feasible mechanism of unwinding duplex RNA. Authors: Cho, H.S. / Ha, N.C. / Kang, L.W. / Chung, K.M. / Back, S.H. / Jang, S.K. / Oh, B.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ohm.cif.gz | 96.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ohm.ent.gz | 71 KB | Display | PDB format |
PDBx/mmJSON format | 8ohm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/8ohm ftp://data.pdbj.org/pub/pdb/validation_reports/oh/8ohm | 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: 46602.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus / Genus: Hepacivirus / Cell line: BL21 / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P26663 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 40 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.8 % | ||||||||||||||||||||
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Crystal grow | pH: 5.6 / Details: pH 5.6 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: batch method | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418 |
Detector | Type: MAC Science DIP-2020 / Detector: IMAGE PLATE / Date: Dec 1, 1997 |
Radiation | Monochromator: CUK / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→15 Å / Num. obs: 23007 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.03 / Rsym value: 0.04 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 14 / Rsym value: 0.2 / % possible all: 92 |
Reflection shell | *PLUS % possible obs: 92 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.3→10 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.01 / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 1895
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 18.4 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS
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