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- PDB-8ago: BK Polyomavirus VP1 mutant E73Q -

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Basic information

Entry
Database: PDB / ID: 8ago
TitleBK Polyomavirus VP1 mutant E73Q
ComponentsMajor capsid protein VP1
KeywordsVIRAL PROTEIN / Patient-derived VP1 mutant
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / T=7 icosahedral viral capsid / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid
Similarity search - Domain/homology
Major capsid protein VP1
Similarity search - Component
Biological speciesBetapolyomavirus hominis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.853 Å
AuthorsSorin, 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
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE17-0003 France
German Research Foundation (DFG)FOR2327 ViroCarb Germany
CitationJournal: 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
DepositionJul 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Major capsid protein VP1
BBB: Major capsid protein VP1
CCC: Major capsid protein VP1
DDD: Major capsid protein VP1
EEE: Major capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,45613
Polymers149,0025
Non-polymers4548
Water15,151841
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23990 Å2
ΔGint-209 kcal/mol
Surface area44270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.253, 153.039, 62.801
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Major capsid protein VP1 / Major structural protein VP1


Mass: 29800.494 Da / Num. of mol.: 5
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 841 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3.350 Lithium Chloride HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.853→50 Å / Num. obs: 119532 / % possible obs: 99.6 % / Redundancy: 13.2 % / CC1/2: 0.999 / Net I/σ(I): 13.99
Reflection shellResolution: 1.853→1.919 Å / Num. unique obs: 11509 / CC1/2: 0.737

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
REFMACphasing
Cootmodel building
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MJ1

4mj1


Resolution: 1.853→48.545 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.197 / WRfactor Rwork: 0.161 / SU B: 3.857 / SU ML: 0.107 / Average fsc free: 0.8837 / Average fsc work: 0.8959 / Cross valid method: FREE R-VALUE / ESU R: 0.14 / ESU R Free: 0.133
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.229 5959 5.001 %
Rwork0.1902 113188 -
all0.192 --
obs-119147 99.602 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.682 Å2
Baniso -1Baniso -2Baniso -3
1--1.062 Å20 Å2-0 Å2
2--1.152 Å2-0 Å2
3----0.089 Å2
Refinement stepCycle: LAST / Resolution: 1.853→48.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9766 0 23 841 10630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01310078
X-RAY DIFFRACTIONr_bond_other_d0.0010.0159246
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.64813726
X-RAY DIFFRACTIONr_angle_other_deg1.3071.57621292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.67951296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7422.928502
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.943151563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9021555
X-RAY DIFFRACTIONr_chiral_restr0.0710.21320
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211648
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022306
X-RAY DIFFRACTIONr_nbd_refined0.2020.21687
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.28686
X-RAY DIFFRACTIONr_nbtor_refined0.1610.24743
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.24895
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2675
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0570.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.220.210
X-RAY DIFFRACTIONr_nbd_other0.2070.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.211
X-RAY DIFFRACTIONr_mcbond_it2.3392.9575151
X-RAY DIFFRACTIONr_mcbond_other2.3392.9575150
X-RAY DIFFRACTIONr_mcangle_it3.2334.4116422
X-RAY DIFFRACTIONr_mcangle_other3.2324.4116423
X-RAY DIFFRACTIONr_scbond_it2.7443.1414927
X-RAY DIFFRACTIONr_scbond_other2.7443.1424928
X-RAY DIFFRACTIONr_scangle_it3.9584.6287292
X-RAY DIFFRACTIONr_scangle_other3.9584.6297293
X-RAY DIFFRACTIONr_lrange_it5.17334.42110721
X-RAY DIFFRACTIONr_lrange_other5.12334.15310569
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.853-1.9010.5224240.49780400.49987720.6010.62496.48880.556
1.901-1.9530.4114240.41480450.41484700.7670.76899.98820.414
1.953-2.0090.2854130.24578590.24782760.8480.86599.95170.218
2.009-2.0710.2484030.21476510.21680540.8910.91000.189
2.071-2.1390.2293920.19974440.20178360.9080.9171000.172
2.139-2.2130.2733750.24271200.24475340.8880.89999.48230.201
2.213-2.2970.3983620.36568790.36773400.8090.82698.65120.338
2.297-2.390.2533510.19666820.19870360.920.93799.95740.156
2.39-2.4960.2393390.17164240.17567630.9230.9431000.141
2.496-2.6180.2053240.15561710.15864950.9460.9551000.129
2.618-2.7590.2163080.15158500.15461580.9430.961000.128
2.759-2.9260.2042920.15555430.15858350.9470.961000.133
2.926-3.1270.2222770.16152550.16455320.940.9571000.142
3.127-3.3760.1712570.15848940.15951510.9630.9641000.144
3.376-3.6970.2292380.17745180.1847620.9410.95899.8740.161
3.697-4.130.1912150.14940930.15143120.9570.96899.90720.138
4.13-4.7640.1591920.12536430.12638350.9720.981000.126
4.764-5.820.1931650.14331310.14532960.9730.9781000.145
5.82-8.1720.1771290.16524640.16525930.9670.971000.166
8.172-48.5450.209790.21514830.21415640.9570.9599.87210.222

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