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Yorodumi- PDB-6wy1: Crystal structure of an engineered thermostable dengue virus 2 en... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wy1 | |||||||||
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Title | Crystal structure of an engineered thermostable dengue virus 2 envelope protein dimer | |||||||||
Components | Dengue 2 soluble recombinant envelope | |||||||||
Keywords | VIRAL PROTEIN / Dengue virus / envelope protein / thermostable / computational protein design / protein engineering | |||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / : / viral capsid / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / : / viral capsid / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / 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 / protein dimerization activity / induction by virus of host autophagy / 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 / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Dengue virus 2 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 Å | |||||||||
Authors | Kudlacek, S.T. / Lakshmanane, P. / Kuhlman, B. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Sci Adv / Year: 2021 Title: Designed, highly expressing, thermostable dengue virus 2 envelope protein dimers elicit quaternary epitope antibodies. Authors: Kudlacek, S.T. / Metz, S. / Thiono, D. / Payne, A.M. / Phan, T.T.N. / Tian, S. / Forsberg, L.J. / Maguire, J. / Seim, I. / Zhang, S. / Tripathy, A. / Harrison, J. / Nicely, N.I. / Soman, S. ...Authors: Kudlacek, S.T. / Metz, S. / Thiono, D. / Payne, A.M. / Phan, T.T.N. / Tian, S. / Forsberg, L.J. / Maguire, J. / Seim, I. / Zhang, S. / Tripathy, A. / Harrison, J. / Nicely, N.I. / Soman, S. / McCracken, M.K. / Gromowski, G.D. / Jarman, R.G. / Premkumar, L. / de Silva, A.M. / Kuhlman, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wy1.cif.gz | 103.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wy1.ent.gz | 66.8 KB | Display | PDB format |
PDBx/mmJSON format | 6wy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/6wy1 ftp://data.pdbj.org/pub/pdb/validation_reports/wy/6wy1 | HTTPS FTP |
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-Related structure data
Related structure data | 1oanS 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: 45694.324 Da / Num. of mol.: 1 / Mutation: G106D, A259W, T262R, F279W, T280P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 2 / Plasmid: P-alphaH / Cell line (production host): EXPI293F / Production host: Homo sapiens (human) / References: UniProt: D0EPS0 |
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#2: Sugar | ChemComp-NAG / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.54 % / Description: Hexagonal plate crystals |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 15% PEG 3350 pH 4.4, 0.1M Sodium Acetate Trihydrate + 0.1M Sodium Iodide Temp details: 21 degree C |
-Data collection
Diffraction | Mean temperature: 193 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2019 / Details: Si 111 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.42→86.58 Å / Num. obs: 9507 / % possible obs: 99.8 % / Redundancy: 16.1 % / Biso Wilson estimate: 92.9 Å2 / CC1/2: 0.982 / Rpim(I) all: 0.162 / Χ2: 1.22 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 3.42→3.69 Å / Redundancy: 16.2 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1901 / CC1/2: 0.693 / Rpim(I) all: 1.264 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OAN Resolution: 3.42→59.67 Å / SU ML: 0.62 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 44.54 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 99.06 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.42→59.67 Å
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Refine LS restraints |
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LS refinement shell |
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