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Yorodumi- PDB-4e76: Apo crystal structure of HCV NS5B genotype 2A JFH-1 isolate with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4.0E+76 | ||||||
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Title | Apo crystal structure of HCV NS5B genotype 2A JFH-1 isolate with beta hairpin loop deletion | ||||||
Components | RNA-directed RNA polymerase | ||||||
Keywords | VIRAL PROTEIN / TRANSFERASE / RDRP / loopless DELTA8 / Flaviviridae / hepatitis C virus | ||||||
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 / 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 / SH3 domain binding ...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 / 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 / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Hepatitis C virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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 | 4e76.cif.gz | 224.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e76.ent.gz | 180.5 KB | Display | PDB format |
PDBx/mmJSON format | 4e76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e76_validation.pdf.gz | 454.2 KB | Display | wwPDB validaton report |
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Full document | 4e76_full_validation.pdf.gz | 460.2 KB | Display | |
Data in XML | 4e76_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 4e76_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/4e76 ftp://data.pdbj.org/pub/pdb/validation_reports/e7/4e76 | HTTPS FTP |
-Related structure data
Related structure data | 4e78C 4e7aC 3i5kS C: citing same article (ref.) S: Starting model for refinement |
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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: 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 | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | Sequence details | PROTEIN COMPRISES UNP RESIDUES 2443-3012 WITH RESIDUES 2886-2895 REPLACED WITH A GG LINKER. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.15 Å3/Da / Density % sol: 70.38 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 3.95 mg/mL NS5B in 20 mM Tris, pH 8, 200 mM sodium chloride, 20% glycerol, 2 mM TCEP, 200 mM imidazole against 30% PEG550 MME, 0.1 M Bis-Tris propane, pH 6.5, 50 mM ammonium sulfate, ...Details: 3.95 mg/mL NS5B in 20 mM Tris, pH 8, 200 mM sodium chloride, 20% glycerol, 2 mM TCEP, 200 mM imidazole against 30% PEG550 MME, 0.1 M Bis-Tris propane, pH 6.5, 50 mM ammonium sulfate, cryoprotectant: 25% ethylene glycol, crystal tracking ID 227386E9, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 / Wavelength: 0.9765 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: asymmetric curved crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. all: 36203 / Num. obs: 34324 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 47.751 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 19.12 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 3I5K Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.1863 / WRfactor Rwork: 0.1507 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7625 / SU B: 19.29 / SU ML: 0.191 / SU R Cruickshank DPI: 0.297 / SU Rfree: 0.2439 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 118.75 Å2 / Biso mean: 45.3948 Å2 / Biso min: 18.45 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.56 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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