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- PDB-5o19: Japanese encephalitis virus non-structural protein 1 C-terminal domain -
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Open data
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Basic information
Entry | Database: PDB / ID: 5o19 | ||||||
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Title | Japanese encephalitis virus non-structural protein 1 C-terminal domain | ||||||
![]() | Genome polyprotein | ||||||
![]() | VIRAL PROTEIN / non-structural protein 1 / Flavivirus protein | ||||||
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 / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Poonsiri, T. / 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 | ![]() | 84.2 KB | Display | ![]() |
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PDB format | ![]() | 63.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.5 KB | Display | ![]() |
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Full document | ![]() | 452.5 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5o36C ![]() 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: 20698.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pET303 / Production host: ![]() ![]() References: UniProt: P27395, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % / Description: needle |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1 M Ammonium sulphate and 0.1 M MES pH 5.5 / PH range: 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→47.3 Å / Num. obs: 18896 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 34.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.045 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.907 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2701 / CC1/2: 0.923 / Rpim(I) all: 0.383 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4oie Resolution: 2.1→47.3 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.183 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.144 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.029 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→47.3 Å
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Refine LS restraints |
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