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Yorodumi- PDB-2zku: Structure of hepatitis C virus NS5B polymerase in a new crystal form -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zku | ||||||
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Title | Structure of hepatitis C virus NS5B polymerase in a new crystal form | ||||||
Components | Genome polyprotein | ||||||
Keywords | TRANSFERASE / HEPATITIS C VIRUS / OLIGOMERISATION / ALLOSTERIC NUCLEOTIDE BINDING SITE / Envelope protein / Helicase / Hydrolase / Nucleotide-binding / RNA replication / Transmembrane | ||||||
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 / ribonucleoside triphosphate phosphatase activity / lipid droplet ...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 / ribonucleoside triphosphate phosphatase activity / lipid droplet / 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 / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Hepatitis C virus subtype 1b | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Biswal, B.K. | ||||||
Citation | Journal: To be Published Title: Structure of Hepatitis C Virus Ns5B Polymerase in a New Crystal Form: Insights Into Oligomerisation and Allosteric Nucleotide Binding Site Authors: Biswal, B.K. / Cherney, M.M. / Chan, L. / Yannopoulos, C.G. / Bilimoria, D. / Bedard, J. / James, M.N.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zku.cif.gz | 478.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zku.ent.gz | 391.7 KB | Display | PDB format |
PDBx/mmJSON format | 2zku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/2zku ftp://data.pdbj.org/pub/pdb/validation_reports/zk/2zku | HTTPS FTP |
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-Related structure data
Related structure data | 1c2pS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 64103.465 Da / Num. of mol.: 4 / Fragment: NS5B POLYMERASE Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus subtype 1b / Strain: BK ISOLATE / Gene: NS5B / Plasmid: PET21B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q99AU2, UniProt: P26663*PLUS, RNA-directed RNA polymerase #2: Chemical | ChemComp-ACY / #3: Chemical | ChemComp-GOL / #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: 2.59 Å3/Da / Density % sol: 52.47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PROTEIN CONCENTRATION 40MG/ML IN 5MM 2-MERCAPTOETHANOL, 18% PEG 4000, 0.3M NACL, 0.1M SODIUM ACETATE BUFFER PH 5.0, 5MM MERCAPTOETHANOL, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115879 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 12, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115879 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→45.64 Å / Num. obs: 185695 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 25.6 Å2 / Rsym value: 0.089 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.54 / Rsym value: 0.705 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1C2P Resolution: 1.95→45.64 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1490093.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.55 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→45.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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