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Yorodumi- PDB-6a0p: Crystal structure of Usutu virus envelope protein in the pre-fusi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a0p | ||||||
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Title | Crystal structure of Usutu virus envelope protein in the pre-fusion state | ||||||
Components | Envelope proteinViral envelope | ||||||
Keywords | VIRAL PROTEIN / Usutu virus / envelope / pre-fusion state / domain-angle difference | ||||||
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 / RNA helicase activity / host cell endoplasmic reticulum membrane / 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 / 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 | Usutu virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Lu, G. / Chen, Z. / Ye, F. / Lin, S. / Yang, F. / Cheng, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Virol. J. / Year: 2018 Title: Crystal structure of Usutu virus envelope protein in the pre-fusion state Authors: Chen, Z. / Ye, F. / Lin, S. / Yang, F. / Cheng, Y. / Cao, Y. / Chen, Z. / Lu, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a0p.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a0p.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 6a0p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/6a0p ftp://data.pdbj.org/pub/pdb/validation_reports/a0/6a0p | HTTPS FTP |
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-Related structure data
Related structure data | 2hg0S S: Starting model for refinement |
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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: 44756.453 Da / Num. of mol.: 1 / Fragment: UNP residues 294-699 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Usutu virus Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q5WPU5 |
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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: 2.38 Å3/Da / Density % sol: 48.22 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, pH 7.5, 10%(w/v) Polyethylene glycol 8,000, and 8%(v/v) Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 29488 / % possible obs: 99.6 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.808 / Num. unique obs: 2838 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HG0 Resolution: 2→30.992 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.32 / 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→30.992 Å
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Refine LS restraints |
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LS refinement shell |
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