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- PDB-8agh: BK Polyomavirus VP1 mutant E73A -

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Basic information

Entry
Database: PDB / ID: 8agh
TitleBK Polyomavirus VP1 mutant E73A
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: 1.887 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
Item: _pdbx_initial_refinement_model.accession_code

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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)149,35515
Polymers148,7175
Non-polymers63810
Water11,277626
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23860 Å2
ΔGint-201 kcal/mol
Surface area44570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.488, 152.305, 62.578
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: 29743.443 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.: 5 / 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.: 626 / 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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3.350 Lithium Chloride HEPES / PH range: 7.5

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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: Sep 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.887→1.935 Å / Num. unique obs: 17862 / CC1/2: 0.69

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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: 1.887→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
RfactorNum. reflection% reflection
Rfree0.2115 5587 5 %
Rwork0.1745 106147 -
all0.176 --
obs-111193 99.888 %
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: 30.446 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å2-0 Å20 Å2
2---0.532 Å20 Å2
3----0.198 Å2
Refinement stepCycle: LAST / Resolution: 1.887→47.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9792 0 35 626 10453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01310115
X-RAY DIFFRACTIONr_bond_other_d0.0010.0159214
X-RAY DIFFRACTIONr_angle_refined_deg1.621.64613783
X-RAY DIFFRACTIONr_angle_other_deg1.3291.57321191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.68651307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61422.889488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2151524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2631553
X-RAY DIFFRACTIONr_chiral_restr0.0720.21333
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211722
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022300
X-RAY DIFFRACTIONr_nbd_refined0.20.21673
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.28801
X-RAY DIFFRACTIONr_nbtor_refined0.1620.24792
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.24951
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2566
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0240.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2030.217
X-RAY DIFFRACTIONr_nbd_other0.2520.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1060.27
X-RAY DIFFRACTIONr_mcbond_it2.63.1855231
X-RAY DIFFRACTIONr_mcbond_other2.5993.1855230
X-RAY DIFFRACTIONr_mcangle_it3.5394.7546528
X-RAY DIFFRACTIONr_mcangle_other3.5384.7546529
X-RAY DIFFRACTIONr_scbond_it3.0923.3724884
X-RAY DIFFRACTIONr_scbond_other3.0923.3724885
X-RAY DIFFRACTIONr_scangle_it4.4234.9637252
X-RAY DIFFRACTIONr_scangle_other4.4224.9647253
X-RAY DIFFRACTIONr_lrange_it5.68636.94310567
X-RAY DIFFRACTIONr_lrange_other5.66836.80810477
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
1.887-1.9350.2914030.28376660.28481770.8040.80798.67920.268
1.935-1.9880.2833980.2575600.25179580.8490.8551000.227
1.988-2.0460.2473870.21973500.2277370.8970.9051000.193
2.046-2.1090.2543770.20871640.2175420.8960.91599.98670.18
2.109-2.1780.2433660.20269460.20473120.9090.9221000.171
2.178-2.2540.2333540.19267250.19470800.9250.92999.98590.16
2.254-2.3390.2243400.18364610.18568010.9290.9371000.149
2.339-2.4340.2183290.17962600.18165890.9330.9431000.148
2.434-2.5420.2453160.18260080.18563240.9230.9431000.147
2.542-2.6660.2153030.17657510.17860540.9390.9471000.145
2.666-2.810.2062900.16555050.16757950.9490.9551000.136
2.81-2.9790.242730.17651870.17954600.9250.9491000.15
2.979-3.1840.2312560.17148740.17451300.9340.9541000.15
3.184-3.4380.2112420.16945890.17148310.9460.9591000.155
3.438-3.7640.2152220.1742160.17244380.9490.9591000.161
3.764-4.2050.172030.14338560.14540590.9670.9721000.141
4.205-4.850.1441790.12534120.12635910.9790.981000.126
4.85-5.9250.1921530.15229110.15430640.9630.9711000.153
5.925-8.3150.2111220.17223120.17424340.9570.9661000.172
8.315-47.8980.187740.20813940.20714720.9480.95399.72830.216

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