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Yorodumi- PDB-4wta: CRYSTAL STRUCTURE OF HCV NS5B GENOTYPE 2A JFH-1 ISOLATE WITH S15G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wta | ||||||
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Title | CRYSTAL STRUCTURE OF HCV NS5B GENOTYPE 2A JFH-1 ISOLATE WITH S15G E86Q E87Q C223H V321I MUTATIONS AND DELTA8 BETA HAIRPIN LOOP DELETION IN COMPLEX WITH UDP, MN2+ AND SYMMETRICAL PRIMER TEMPLATE 5'-CAAAAUUU | ||||||
Components |
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Keywords | Transferase/RNA / HCV / VIRAL / NS5B / RDRP / RESISTANCE MUTATION / TEMPLATE / PRIMER / PRIMED INITIATION / DELTA8 BETA HAIRPIN LOOP DELETION / Transferase-RNA complex | ||||||
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 / serine-type endopeptidase activity / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / apoptotic process / 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 JFH-1 synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 | 4wta.cif.gz | 131.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wta.ent.gz | 96.3 KB | Display | PDB format |
PDBx/mmJSON format | 4wta.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wta_validation.pdf.gz | 825.1 KB | Display | wwPDB validaton report |
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Full document | 4wta_full_validation.pdf.gz | 828.5 KB | Display | |
Data in XML | 4wta_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 4wta_validation.cif.gz | 30 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/4wta ftp://data.pdbj.org/pub/pdb/validation_reports/wt/4wta | HTTPS FTP |
-Related structure data
Related structure data | 4wt9C 4wtcC 4wtdC 4wteC 4wtfC 4wtgC 4wtiC 4wtjC 4wtkC 4wtlC 4wtmC 4obcS 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
-RNA chain / Protein , 2 types, 3 molecules TPA
#1: RNA chain | Mass: 2495.545 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: 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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-Non-polymers , 4 types, 71 molecules
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-UDP / | #6: 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: 4 Å3/Da / Density % sol: 70 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: NS5B AT 5.1 MG/ML IN 5 MM TRIS PH 7.5, 200 MM NH4OAC, 1 MM EDTA, 1 MM DTT AGAINST 25% PEG 550 MME, 50 MM MGCL2, 0.1 M HEPES PH 7.5 FOR CRYSTAL GROWTH SOAKED INTO 28% PEG 550 MME, 0.2 M ...Details: NS5B AT 5.1 MG/ML IN 5 MM TRIS PH 7.5, 200 MM NH4OAC, 1 MM EDTA, 1 MM DTT AGAINST 25% PEG 550 MME, 50 MM MGCL2, 0.1 M HEPES PH 7.5 FOR CRYSTAL GROWTH SOAKED INTO 28% PEG 550 MME, 0.2 M AMMONIUM ACETATE, 0.05 M BISTRIS PROPANE PH 6.0, 0.05 M TRIS PH 7.2, 6 MM MNCL2, 10 MM UDP, 2 MM 5'-CAAAAUUU WITH 8% GLYCEROL AS CRYO-PROTECTANT, CRYSTAL TRACKING ID 251148C3, UNIQUE PUCK ID DDL1-9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 25310 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 52.19 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.088 / Χ2: 0.952 / Net I/σ(I): 22.27 / Num. measured all: 140462 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 5.6 % / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 3.3 / Num. measured obs: 1307 / Num. possible: 306 / Num. unique obs: 291 / Rrim(I) all: 0.02 / Rejects: 0 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OBC Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.916 / SU B: 11.725 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.42 / ESU R Free: 0.274 / 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: 123.29 Å2 / Biso mean: 52.49 Å2 / Biso min: 27.03 Å2
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Refinement step | Cycle: final / Resolution: 2.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.87 Å / Total num. of bins used: 20
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