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Open data
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Basic information
Entry | Database: PDB / ID: 8agh | |||||||||
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Title | BK Polyomavirus VP1 mutant E73A | |||||||||
![]() | Major capsid protein VP1 | |||||||||
![]() | VIRAL PROTEIN / Patient-derived VP1 mutant | |||||||||
Function / homology | ![]() caveolin-mediated endocytosis of virus by host cell / T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sorin, M.N. / Di Maio, A. / Silva, L.M. / Ebert, D. / Delannoy, C. / Nguyen, N.-K. / Guerardel, Y. / Chai, W. / Halary, F. / Renaudin-Autain, K. ...Sorin, M.N. / Di Maio, A. / Silva, L.M. / Ebert, D. / Delannoy, C. / Nguyen, N.-K. / Guerardel, Y. / Chai, W. / Halary, F. / Renaudin-Autain, K. / Liu, Y. / Bressollette-Bodin, C. / Stehle, T. / McIlroy, D. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structural and functional analysis of natural capsid variants suggests sialic acid-independent entry of BK polyomavirus. Authors: Sorin, M.N. / Di Maio, A. / Silva, L.M. / Ebert, D. / Delannoy, C.P. / Nguyen, N.K. / Guerardel, Y. / Chai, W. / Halary, F. / Renaudin-Autain, K. / Liu, Y. / Bressollette-Bodin, C. / Stehle, T. / McIlroy, D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 277.5 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.3 KB | Display | ![]() |
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Full document | ![]() | 482.9 KB | Display | |
Data in XML | ![]() | 51.8 KB | Display | |
Data in CIF | ![]() | 73.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8agoC ![]() 8ah0C ![]() 8ah1C ![]() 4mj1S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29743.443 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.3 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3.350 Lithium Chloride HEPES / PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.887→50 Å / Num. obs: 111193 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 0.99 / Net I/σ(I): 15.63 |
Reflection shell | Resolution: 1.887→1.935 Å / Num. unique obs: 17862 / CC1/2: 0.69 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4MJ1 Resolution: 1.887→47.898 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.575 / SU ML: 0.101 / Cross valid method: FREE R-VALUE / ESU R: 0.136 / ESU R Free: 0.128 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.446 Å2
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Refinement step | Cycle: LAST / Resolution: 1.887→47.898 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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