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Yorodumi- PDB-8ufn: Crystal Structure of neuronal HAstV VA1 capsid spike domain at 2.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ufn | ||||||
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Title | Crystal Structure of neuronal HAstV VA1 capsid spike domain at 2.73 A resolution | ||||||
Components | Capsid polyprotein VP90 | ||||||
Keywords | VIRAL PROTEIN / Human Astrovirus / Capsid spike domain / Antigenicity | ||||||
Function / homology | Capsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / T=3 icosahedral viral capsid / Viral coat protein subunit / clathrin-dependent endocytosis of virus by host cell / Capsid polyprotein VP90 Function and homology information | ||||||
Biological species | Astrovirus VA1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å | ||||||
Authors | Ghosh, A. / Delgado-Cunningham, K. / DuBois, R.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Plos Pathog. / Year: 2024 Title: Structure and antigenicity of the divergent human astrovirus VA1 capsid spike. Authors: Ghosh, A. / Delgado-Cunningham, K. / Lopez, T. / Green, K. / Arias, C.F. / DuBois, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ufn.cif.gz | 143.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ufn.ent.gz | 89.6 KB | Display | PDB format |
PDBx/mmJSON format | 8ufn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ufn_validation.pdf.gz | 438.5 KB | Display | wwPDB validaton report |
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Full document | 8ufn_full_validation.pdf.gz | 452.1 KB | Display | |
Data in XML | 8ufn_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 8ufn_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/8ufn ftp://data.pdbj.org/pub/pdb/validation_reports/uf/8ufn | HTTPS FTP |
-Related structure data
Related structure data | 8ufoC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34500.594 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Astrovirus VA1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D7P3D4 |
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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: 2.08 Å3/Da / Density % sol: 40.95 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 27.5% PEG3350 / PH range: 7-8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.03 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→46.04 Å / Num. obs: 15883 / % possible obs: 99.93 % / Redundancy: 13 % / Biso Wilson estimate: 44.17 Å2 / CC1/2: 0.989 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.73→2.86 Å / Num. unique obs: 1541 / CC1/2: 0.616 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→46.04 Å / SU ML: 0.4613 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.7654 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.73→46.04 Å
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Refine LS restraints |
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LS refinement shell |
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