+Open data
-Basic information
Entry | Database: PDB / ID: 6izy | |||||||||
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Title | The RNA-dependent RNA polymerase domain of dengue 2 NS5 | |||||||||
Components | Genome polyprotein | |||||||||
Keywords | VIRAL PROTEIN / Dengue / NS5 / RNA-dependent RNA polymerase | |||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / 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 / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Dengue virus 2 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.11 Å | |||||||||
Authors | Shimizu, H. / Sekine, S. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Plos Negl Trop Dis / Year: 2019 Title: Discovery of a small molecule inhibitor targeting dengue virus NS5 RNA-dependent RNA polymerase. Authors: Shimizu, H. / Saito, A. / Mikuni, J. / Nakayama, E.E. / Koyama, H. / Honma, T. / Shirouzu, M. / Sekine, S.I. / Shioda, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6izy.cif.gz | 142.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6izy.ent.gz | 108.3 KB | Display | PDB format |
PDBx/mmJSON format | 6izy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6izy_validation.pdf.gz | 438.6 KB | Display | wwPDB validaton report |
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Full document | 6izy_full_validation.pdf.gz | 443.8 KB | Display | |
Data in XML | 6izy_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 6izy_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/6izy ftp://data.pdbj.org/pub/pdb/validation_reports/iz/6izy | HTTPS FTP |
-Related structure data
Related structure data | 6izxC 6izzC 6j00C 2j7uS 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: 79627.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 2 / Production host: Escherichia coli KRX (bacteria) / References: UniProt: C6L435, UniProt: P14340*PLUS | ||||||
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#2: Chemical | ChemComp-CO / #3: Chemical | ChemComp-ZN / | #4: Water | ChemComp-HOH / | Sequence details | The 244-250 seq derived from the protease site. The protein seq is identical to GenBank ACQ44526.1. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.69 Å3/Da / Density % sol: 66.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.6 M ammonium sulfate, 100 mM MES-NaOH (pH 6.2-6.5), and 10 mM CoCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→53.14 Å / Num. obs: 65159 / % possible obs: 95.7 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rsym value: 0.058 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 2.11→2.16 Å / Num. unique obs: 3092 / CC1/2: 0.398 / Rsym value: 1.487 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2J7U Resolution: 2.11→41.958 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.15
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 158.82 Å2 / Biso mean: 56.1535 Å2 / Biso min: 27.84 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.11→41.958 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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