+Open data
-Basic information
Entry | Database: PDB / ID: 6j00 | |||||||||
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Title | The RNA-dependent RNA polymerase domain of dengue 3 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 / 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 / : / viral capsid / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / : / viral capsid / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / 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 endoplasmic reticulum membrane / protein dimerization activity / induction by virus of host autophagy / viral RNA genome replication / 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 / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Dengue virus 3 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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 | 6j00.cif.gz | 139.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j00.ent.gz | 103.7 KB | Display | PDB format |
PDBx/mmJSON format | 6j00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/6j00 ftp://data.pdbj.org/pub/pdb/validation_reports/j0/6j00 | HTTPS FTP |
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-Related structure data
Related structure data | 6izxC 6izyC 6izzC 2j7uS 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: 74798.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 3 / Production host: Escherichia coli KRX (bacteria) / References: UniProt: Q5I3C1 | ||
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#2: Chemical | #3: 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: 2.85 Å3/Da / Density % sol: 56.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 16% polyethylene glycol 10000 and 100 mM Tris-HCl (pH 8.0) |
-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: Sep 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→62.7 Å / Num. obs: 46398 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rsym value: 0.133 / Net I/σ(I): 12.06 |
Reflection shell | Resolution: 2.14→2.2 Å / Num. unique obs: 3359 / CC1/2: 0.616 / Rsym value: 1.541 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2J7U Resolution: 2.14→51.519 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.14→51.519 Å
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LS refinement shell | Resolution: 2.14→2.2 Å /
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