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Yorodumi- PDB-1a1v: HEPATITIS C VIRUS NS3 HELICASE DOMAIN COMPLEXED WITH SINGLE STRAN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a1v | ||||||
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Title | HEPATITIS C VIRUS NS3 HELICASE DOMAIN COMPLEXED WITH SINGLE STRANDED SDNA | ||||||
Components |
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Keywords | HYDROLASE/DNA / HEPATITIS C VIRUS / RNA HELICASE / NONSTRUCTURAL PROTEINS / SINGLE-STRANDED DNA / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet ...positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / positive regulation of cytokinesis / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / negative regulation of protein secretion / 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 / endoplasmic reticulum-Golgi intermediate compartment membrane / SH3 domain binding / kinase binding / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / entry receptor-mediated virion attachment to host cell / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / RNA helicase / induction by virus of host autophagy / ribonucleoprotein complex / RNA-directed RNA polymerase / 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 / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Hepatitis C virus | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.2 Å | ||||||
Authors | Kim, J.L. / Morgenstern, K.A. / Griffith, J.P. / Dwyer, M.D. / Thomson, J.A. / Murcko, M.A. / Lin, C. / Caron, P.R. | ||||||
Citation | Journal: Structure / Year: 1998 Title: Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: the crystal structure provides insights into the mode of unwinding. Authors: Kim, J.L. / Morgenstern, K.A. / Griffith, J.P. / Dwyer, M.D. / Thomson, J.A. / Murcko, M.A. / Lin, C. / Caron, P.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a1v.cif.gz | 115.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a1v.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 1a1v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/1a1v ftp://data.pdbj.org/pub/pdb/validation_reports/a1/1a1v | 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: DNA chain | Mass: 2276.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC DEOXYOLIGONUCLEOTIDE |
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#2: Protein | Mass: 51362.285 Da / Num. of mol.: 1 / Fragment: HELICASE DOMAIN Mutation: N-TERMINAL MET, K221Q, A277G, S301L, S332P, S410A, G530E, R582W, AND A 10 RESIDUE (GSGSHHHHHH) HISTIDINE TAG ATTACHED TO THE C-TERMINUS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus (isolate H) / Genus: Hepacivirus / Species: Hepatitis C virus / Strain: H / Gene: NS3 / Plasmid: PET-BS(+) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P27958 |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS 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 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 15, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→35 Å / Num. obs: 31255 / % possible obs: 95.5 % / Observed criterion σ(I): -1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 5.9 / Rsym value: 0.138 / % possible all: 81.7 |
Reflection shell | *PLUS % possible obs: 81.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.2→6 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 29.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.27 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.278 |