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- PDB-7zip: JC Polyomavirus VP1 in complex with 3'-Sialyllactose glycomacromo... -

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Basic information

Entry
Database: PDB / ID: 7zip
TitleJC Polyomavirus VP1 in complex with 3'-Sialyllactose glycomacromolecules (aliphatic linker)
ComponentsMajor capsid protein VP1
KeywordsVIRAL PROTEIN / Complex / Sialic acid / Capsid protein
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
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: 1.9 Å
AuthorsFreytag, J. / Mueller, J.C. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2327 Germany
CitationJournal: Biomacromolecules / Year: 2022
Title: Synthesis of Homo- and Heteromultivalent Fucosylated and Sialylated Oligosaccharide Conjugates via Preactivated N -Methyloxyamine Precision Macromolecules and Their Binding to Polyomavirus Capsid Proteins.
Authors: Konietzny, P.B. / Freytag, J. / Feldhof, M.I. / Muller, J.C. / Ohl, D. / Stehle, T. / Hartmann, L.
History
DepositionApr 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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

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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)151,9396
Polymers151,3055
Non-polymers6341
Water14,700816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23200 Å2
ΔGint-155 kcal/mol
Surface area45080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.734, 152.505, 62.952
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: 30261.039 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: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 633.552 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: BIRD: PRD_002415
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 816 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5, 0.25 M LiCl, 18% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.9→48 Å / Num. obs: 110486 / % possible obs: 99.9 % / Redundancy: 7.42 % / CC1/2: 0.99 / Rrim(I) all: 0.13 / Net I/σ(I): 13.04
Reflection shellResolution: 1.9→2.01 Å / Num. unique obs: 17558 / CC1/2: 0.63 / Rrim(I) all: 1.27

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MJ1

4mj1


Resolution: 1.9→47.963 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.857 / SU ML: 0.108 / Cross valid method: FREE R-VALUE / ESU R: 0.139 / ESU R Free: 0.133
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2155 5525 5.001 %
Rwork0.1721 104961 -
all0.174 --
obs-110486 99.905 %
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: 26.791 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å20 Å2
2---0.442 Å20 Å2
3----0.869 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9805 0 32 816 10653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01310185
X-RAY DIFFRACTIONr_bond_other_d0.0020.0179078
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.65413906
X-RAY DIFFRACTIONr_angle_other_deg1.3471.57321149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.68251317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04122.97505
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5151585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2811555
X-RAY DIFFRACTIONr_chiral_restr0.0710.21355
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211546
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022048
X-RAY DIFFRACTIONr_nbd_refined0.20.21678
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.28496
X-RAY DIFFRACTIONr_nbtor_refined0.160.24793
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.24367
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2589
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1570.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1790.28
X-RAY DIFFRACTIONr_nbd_other0.2210.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1330.210
X-RAY DIFFRACTIONr_mcbond_it2.1162.7655181
X-RAY DIFFRACTIONr_mcbond_other2.1162.7645180
X-RAY DIFFRACTIONr_mcangle_it3.0264.1246467
X-RAY DIFFRACTIONr_mcangle_other3.0264.1256468
X-RAY DIFFRACTIONr_scbond_it2.7182.9865004
X-RAY DIFFRACTIONr_scbond_other2.7172.9855002
X-RAY DIFFRACTIONr_scangle_it4.054.3877419
X-RAY DIFFRACTIONr_scangle_other4.0484.3877419
X-RAY DIFFRACTIONr_lrange_it5.32132.2610766
X-RAY DIFFRACTIONr_lrange_other5.27232.06210664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9480.3394000.3157585X-RAY DIFFRACTION99.1187
1.948-2.0020.2873920.2597451X-RAY DIFFRACTION100
2.002-2.060.2673830.237279X-RAY DIFFRACTION100
2.06-2.1230.243720.2147077X-RAY DIFFRACTION100
2.123-2.1920.2633620.1986882X-RAY DIFFRACTION99.9724
2.192-2.2690.233490.1866621X-RAY DIFFRACTION99.9857
2.269-2.3550.2243390.1786446X-RAY DIFFRACTION100
2.355-2.4510.2283250.1716169X-RAY DIFFRACTION99.9692
2.451-2.5590.2493120.1725935X-RAY DIFFRACTION100
2.559-2.6840.2293000.165691X-RAY DIFFRACTION99.9833
2.684-2.8280.22850.1525423X-RAY DIFFRACTION99.9825
2.828-2.9990.2082720.1585169X-RAY DIFFRACTION99.9449
2.999-3.2060.2152530.1634800X-RAY DIFFRACTION99.8617
3.206-3.4610.2082380.1664528X-RAY DIFFRACTION100
3.461-3.790.2012200.1634168X-RAY DIFFRACTION100
3.79-4.2340.1622000.1343815X-RAY DIFFRACTION100
4.234-4.8820.1441780.123378X-RAY DIFFRACTION100
4.882-5.9640.1911510.1612875X-RAY DIFFRACTION99.967
5.964-8.370.2481210.1862290X-RAY DIFFRACTION99.8757
8.37-47.9630.257730.21379X-RAY DIFFRACTION99.8624

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