+Open data
-Basic information
Entry | Database: PDB / ID: 8ah1 | |||||||||
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Title | BK Polyomavirus VP1 mutant N-Q | |||||||||
Components | Major capsid protein VP1 | |||||||||
Keywords | VIRAL PROTEIN / Patient-derived VP1 mutant | |||||||||
Function / homology | Function and homology information 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 | Betapolyomavirus hominis | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.006 Å | |||||||||
Authors | 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 | France, Germany, 2items
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Citation | Journal: Cell Rep / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ah1.cif.gz | 528.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ah1.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ah1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/8ah1 ftp://data.pdbj.org/pub/pdb/validation_reports/ah/8ah1 | HTTPS FTP |
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-Related structure data
Related structure data | 8aghC 8agoC 8ah0C 4mj1S C: citing same article (ref.) S: Starting model for refinement |
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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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29785.416 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Betapolyomavirus hominis / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03088 #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.23 Å3/Da / Density % sol: 44.96 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3.350 Lithium Chloride HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 15, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.006→50 Å / Num. obs: 164438 / % possible obs: 94.81 % / Redundancy: 6.6 % / CC1/2: 0.994 / Net I/σ(I): 8.35 |
Reflection shell | Resolution: 2.006→2.082 Å / Num. unique obs: 17100 / CC1/2: 0.852 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MJ1 Resolution: 2.006→48.784 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.093 / SU ML: 0.156 / Cross valid method: FREE R-VALUE / ESU R: 0.199 / ESU R Free: 0.176 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: 28.332 Å2
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Refinement step | Cycle: LAST / Resolution: 2.006→48.784 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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