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Yorodumi- PDB-5mv1: Crystal structure of the E protein of the Japanese encephalitis v... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mv1 | ||||||
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Title | Crystal structure of the E protein of the Japanese encephalitis virulent 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 / double-stranded RNA binding / 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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 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 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 / serine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / 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 | Japanese encephalitis virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 | 5mv1.cif.gz | 169.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mv1.ent.gz | 133.4 KB | Display | PDB format |
PDBx/mmJSON format | 5mv1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mv1_validation.pdf.gz | 425.1 KB | Display | wwPDB validaton report |
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Full document | 5mv1_full_validation.pdf.gz | 431.9 KB | Display | |
Data in XML | 5mv1_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 5mv1_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mv/5mv1 ftp://data.pdbj.org/pub/pdb/validation_reports/mv/5mv1 | HTTPS FTP |
-Related structure data
Related structure data | 5mv2C 3p54S 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: 43764.266 Da / Num. of mol.: 1 / Fragment: UNP residues 295-700 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Japanese encephalitis virus (strain SA-14) Production host: Escherichia coli (E. coli) / References: UniProt: P27395 |
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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: 2.39 Å3/Da / Density % sol: 48.55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris-HCI, pH 8.0, 16% PEG 1000, 0.3M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 21345 / % possible obs: 98.9 % / Redundancy: 4.4 % / CC1/2: 0.99 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 4.6 % / CC1/2: 0.38 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3P54 Resolution: 2.25→19.746 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→19.746 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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