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- PDB-5o36: Japanese encephalitis virus non-structural protein 1' C-terminal ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5o36 | ||||||
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Title | Japanese encephalitis virus non-structural protein 1' C-terminal domain | ||||||
![]() | Japanese encephalitis virus non-structural protein 1' (NS1'),Japanese encephalitis virus non-structural protein 1' (NS1') | ||||||
![]() | VIRAL PROTEIN / Flavivirus protein / NS1' / Japanese encephalitis | ||||||
Function / homology | ![]() 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 / 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 / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thanalai, P. / Wright, G.S.A. / Antonyuk, S.V. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.3 KB | Display | ![]() |
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PDB format | ![]() | 38.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.5 KB | Display | ![]() |
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Full document | ![]() | 447.2 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 13.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5o19C ![]() 4oieS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-POL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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