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Yorodumi- PDB-6s94: Crystal structure of group D of Usutu virus envelope protein doma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s94 | ||||||
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Title | Crystal structure of group D of Usutu virus envelope protein domain III | ||||||
Components | Genome polyprotein | ||||||
Keywords | VIRAL PROTEIN / DIII / Usutu virus / USUV / envelope protein | ||||||
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 / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 ...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 / ribonucleoside triphosphate phosphatase 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 / membrane => GO:0016020 / 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 / molecular replacement / Resolution: 1.79 Å | ||||||
Authors | Schoenenwald, A.K.J. / Skern, T. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Virology / Year: 2020 Title: Structural and antigenic investigation of Usutu virus envelope protein domain III. Authors: Josephine Schoenenwald, A.K. / Pletzer, M. / Skern, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s94.cif.gz | 57.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s94.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 6s94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s9/6s94 ftp://data.pdbj.org/pub/pdb/validation_reports/s9/6s94 | HTTPS FTP |
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-Related structure data
Related structure data | 6s92C 6s93C 6s95SC 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: 11022.431 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Usutu virus / Plasmid: pET11D / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): solu / References: UniProt: S4Z121, UniProt: Q5WPU5*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.88 % / Description: rods |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: NH4 Acet, MES, PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 13, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.79→53.036 Å / Num. all: 17355 / Num. obs: 17355 / % possible obs: 99.5 % / Redundancy: 4.8 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.06 / Rsym value: 0.054 / Net I/av σ(I): 9.3 / Net I/σ(I): 16.2 / Num. measured all: 83419 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6S95 Resolution: 1.79→36.7 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 62.39 Å2 / Biso mean: 25.334 Å2 / Biso min: 9.43 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→36.7 Å
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LS refinement shell | Resolution: 1.79→1.854 Å /
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