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Yorodumi- PDB-5o36: Japanese encephalitis virus non-structural protein 1' C-terminal ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o36 | ||||||
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Title | Japanese encephalitis virus non-structural protein 1' C-terminal domain | ||||||
Components | Japanese encephalitis virus non-structural protein 1' (NS1'),Japanese encephalitis virus non-structural protein 1' (NS1') | ||||||
Keywords | VIRAL PROTEIN / Flavivirus protein / NS1' / Japanese encephalitis | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / host cell surface / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / 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 / virus-mediated perturbation of host defense response / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Japanese encephalitis virus strain SA-14 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Thanalai, P. / Wright, G.S.A. / Antonyuk, S.V. | ||||||
Citation | Journal: J. Virol. / Year: 2018 Title: Structural Study of the C-Terminal Domain of Nonstructural Protein 1 from Japanese Encephalitis Virus. Authors: Poonsiri, T. / Wright, G.S.A. / Diamond, M.S. / Turtle, L. / Solomon, T. / Antonyuk, S.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o36.cif.gz | 55.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o36.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 5o36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/5o36 ftp://data.pdbj.org/pub/pdb/validation_reports/o3/5o36 | HTTPS FTP |
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-Related structure data
Related structure data | 5o19C 4oieS 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: 26014.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Japanese encephalitis virus strain SA-14 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P27395, UniProt: P0DOH7*PLUS | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-POL / | #4: 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: 3.38 Å3/Da / Density % sol: 63.65 % / Description: needle |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.0 M Ammonium sulfate, 5% (v/v) propanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→81.75 Å / Num. obs: 10247 / % possible obs: 99.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 38.6 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.141 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.413 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1203 / CC1/2: 0.462 / Rpim(I) all: 1.03 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4oie Resolution: 2.6→81.75 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.101 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 39.397 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→81.75 Å
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