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Yorodumi- PDB-4e7a: Crystal structure of a product state assembly of HCV NS5B genotyp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4e7a | ||||||
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Title | Crystal structure of a product state assembly of HCV NS5B genotype 2a JFH-1 isolate with beta hairpin deletion bound to primer-template RNA with a 2',3'-ddC | ||||||
Components |
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Keywords | VIRAL PROTEIN / TRANSFERASE/RNA / RDRP / loopless DELTA8 / ternary complex / product complex / Flaviviridae / hepatitis C virus / TRANSFERASE-RNA complex | ||||||
Function / homology | Function and homology information negative regulation of autophagy of mitochondrion / : / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / Dectin-2 family / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity ...negative regulation of autophagy of mitochondrion / : / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / Dectin-2 family / 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 / negative regulation of autophagy / SH3 domain 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 / 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 / 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 / identical protein binding Similarity search - Function | ||||||
Biological species | Hepatitis C virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å | ||||||
Authors | Edwards, T.E. / Mosley, R.T. | ||||||
Citation | Journal: J.Virol. / Year: 2012 Title: Structure of hepatitis C virus polymerase in complex with primer-template RNA. Authors: Mosley, R.T. / Edwards, T.E. / Murakami, E. / Lam, A.M. / Grice, R.L. / Du, J. / Sofia, M.J. / Furman, P.A. / Otto, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e7a.cif.gz | 125.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e7a.ent.gz | 92.7 KB | Display | PDB format |
PDBx/mmJSON format | 4e7a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/4e7a ftp://data.pdbj.org/pub/pdb/validation_reports/e7/4e7a | HTTPS FTP |
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-Related structure data
Related structure data | 4e76SC 4e78C 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: DNA/RNA hybrid | Mass: 2164.372 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | | Mass: 63736.203 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: E86Q, E87Q, Delta8 replaced with GG Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus / Strain: JFH-1 / Gene: NS5B / Plasmid: VCID 5854 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99IB8, RNA-directed RNA polymerase #3: Water | ChemComp-HOH / | Sequence details | PROTEIN COMPRISES UNP RESIDUES 2443-3012 WITH RESIDUES 2886-2895 REPLACED WITH A GG LINKER. | |
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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: 3.95 Å3/Da / Density % sol: 68.88 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 4.37 mg/mL NS5B in 20 mM Tris, pH 8, 200 mM sodium chloride, 20% glycerol, 2 mM TCEP, 200 mM imidazole against 30% PEG3350, 0.1 M Bis-Tris propane, pH 6.0, 200 mM ammonium acetate soaked ...Details: 4.37 mg/mL NS5B in 20 mM Tris, pH 8, 200 mM sodium chloride, 20% glycerol, 2 mM TCEP, 200 mM imidazole against 30% PEG3350, 0.1 M Bis-Tris propane, pH 6.0, 200 mM ammonium acetate soaked overnight in precipitant supplemented with 15% ethylene glycol as cryoprotectant and 0.2 mM CUAGGC(DOC), crystal tracking ID 228018H11, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97956 / Wavelength: 0.97856 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 16, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3→50 Å / Num. all: 21395 / Num. obs: 21289 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 59.238 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 16.76 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4E76 Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.1992 / WRfactor Rwork: 0.1617 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8146 / SU B: 15.182 / SU ML: 0.272 / SU R Cruickshank DPI: 0.6872 / SU Rfree: 0.3375 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.687 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 133.74 Å2 / Biso mean: 55.3872 Å2 / Biso min: 22.43 Å2
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.08 Å / Total num. of bins used: 20
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