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Yorodumi- PDB-5mv2: Crystal structure of the E protein of the Japanese encephalitis l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mv2 | ||||||
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Title | Crystal structure of the E protein of the Japanese encephalitis live attenuated vaccine virus | ||||||
Components | E protein | ||||||
Keywords | VIRAL PROTEIN / viral envelope glycoprotein | ||||||
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 / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 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 / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 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 / host cell surface / RNA helicase activity / host cell endoplasmic reticulum membrane / membrane => GO:0016020 / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Japanese encephalitis virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Liu, X. / Zhao, X. / Na, R. / Li, L. / Warkentin, E. / Witt, J. / Lu, X. / Wei, Y. / Peng, G. / Li, Y. / Wang, J. | ||||||
Citation | Journal: Protein Cell / Year: 2019 Title: The structure differences of Japanese encephalitis virus SA14 and SA14-14-2 E proteins elucidate the virulence attenuation mechanism. Authors: Liu, X. / Zhao, X. / Na, R. / Li, L. / Warkentin, E. / Witt, J. / Lu, X. / Yu, Y. / Wei, Y. / Peng, G. / Li, Y. / Wang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mv2.cif.gz | 174.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mv2.ent.gz | 137.9 KB | Display | PDB format |
PDBx/mmJSON format | 5mv2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mv/5mv2 ftp://data.pdbj.org/pub/pdb/validation_reports/mv/5mv2 | HTTPS FTP |
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-Related structure data
Related structure data | 5mv1SC 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: 44826.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Japanese encephalitis virus (strain SA-14) Strain: SA-14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8QQT1, UniProt: P27395*PLUS |
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#2: 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: 2.72 Å3/Da / Density % sol: 54.81 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.9 / Details: 0.2M Tri-Na citrate, pH 7.9, 18% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97621 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97621 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 28195 / % possible obs: 98.7 % / Redundancy: 6.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.144 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.1 / CC1/2: 0.877 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5mv1 Resolution: 2.1→19.944 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→19.944 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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