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Yorodumi- PDB-4wt9: APO CRYSTAL STRUCTURE OF HCV NS5B GENOTYPE 2A JFH-1 ISOLATE WITH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wt9 | ||||||
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Title | APO CRYSTAL STRUCTURE OF HCV NS5B GENOTYPE 2A JFH-1 ISOLATE WITH E86Q E87Q S15G C223H V321I AND DELTA8 MUTATIONS | ||||||
Components | RNA-directed RNA polymeraseRNA-dependent RNA polymerase | ||||||
Keywords | TRANSFERASE / HCV / VIRAL / NS5B / RDRP / RESISTANCE MUTATION / DELTA8 BETA HAIRPIN LOOP DELETION | ||||||
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 JFH-1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Edwards, T.E. / Appleby, T.C. | ||||||
Citation | Journal: Science / Year: 2015 Title: Structural basis for RNA replication by the hepatitis C virus polymerase. Authors: Appleby, T.C. / Perry, J.K. / Murakami, E. / Barauskas, O. / Feng, J. / Cho, A. / Fox, D. / Wetmore, D.R. / McGrath, M.E. / Ray, A.S. / Sofia, M.J. / Swaminathan, S. / Edwards, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wt9.cif.gz | 125.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wt9.ent.gz | 94.2 KB | Display | PDB format |
PDBx/mmJSON format | 4wt9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/4wt9 ftp://data.pdbj.org/pub/pdb/validation_reports/wt/4wt9 | HTTPS FTP |
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-Related structure data
Related structure data | 4wtaC 4wtcC 4wtdC 4wteC 4wtfC 4wtgC 4wtiC 4wtjC 4wtkC 4wtlC 4wtmC 4e76S 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: Protein | Mass: 63755.211 Da / Num. of mol.: 1 Mutation: S2457G, E2528Q, E2529Q, C2665H, V2763I, UNP residues 2886-2895 NFEMYGSVYS deleted and replaced by GG linker Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus JFH-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99IB8, RNA-directed RNA polymerase |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-EPE / |
#4: Chemical | ChemComp-PG6 / |
#5: 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: 4 Å3/Da / Density % sol: 70 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: NS5B AT 4.08 MG/ML IN 20 MM TRIS PH 8, 200 MM NACL, 20% GLYCEROL, 2 MM TCEP, 200 MM IMIDAZOLE AGAINST 30% PEG 550 MME, 0.1 M HEPES PH 7.5, 50 MM MAGNESIUM CHLORIDE WITH 15% ETHYLENE GLYCOL ...Details: NS5B AT 4.08 MG/ML IN 20 MM TRIS PH 8, 200 MM NACL, 20% GLYCEROL, 2 MM TCEP, 200 MM IMIDAZOLE AGAINST 30% PEG 550 MME, 0.1 M HEPES PH 7.5, 50 MM MAGNESIUM CHLORIDE WITH 15% ETHYLENE GLYCOL AS CRYO-PROTECTANT, CRYSTAL TRACKING ID 232769E7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07809 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 28, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07809 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 35345 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 46.96 Å2 / Rmerge F obs: 0.158 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.099 / Χ2: 0.973 / Net I/σ(I): 16.62 / Num. measured all: 127140 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 3.7 % / Rmerge F obs: 0.016 / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 2.6 / Num. measured obs: 1268 / Num. possible: 426 / Num. unique obs: 394 / Rrim(I) all: 0.021 / Rejects: 0 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4E76 Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / SU B: 8.197 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.227 / 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: 102.63 Å2 / Biso mean: 33.09 Å2 / Biso min: 14.72 Å2
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Refinement step | Cycle: final / 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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