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- PDB-7ziq: BK Polyomavirus VP1 in complex with 6'-Sialyllactose glycomacromo... -

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Basic information

Entry
Database: PDB / ID: 7ziq
TitleBK Polyomavirus VP1 in complex with 6'-Sialyllactose glycomacromolecules (aromatic linker)
ComponentsCapsid protein VP1
KeywordsVIRAL PROTEIN / Complex / Sialic acid / Capsid protein
Function / homology
Function and homology information


T=7 icosahedral viral capsid / 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
DI(HYDROXYETHYL)ETHER / N-acetyl-alpha-neuraminic acid / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)152,91213
Polymers151,3055
Non-polymers1,6068
Water13,475748
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25510 Å2
ΔGint-135 kcal/mol
Surface area44770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.327, 151.838, 63.052
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 5 molecules AAABBBCCCDDDEEE

#1: Protein
Capsid protein VP1 /


Mass: 30261.039 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Betapolyomavirus hominis / Gene: VP1, vp1, BK1035_00004, BK1055_00004 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q65613

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Sugars , 2 types, 3 molecules

#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 633.552 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpb1-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_b6-c2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID / Sialic acid


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 753 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 748 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.28 Å3/Da / Density % sol: 46.12 %
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→48.5 Å / Num. obs: 110045 / % possible obs: 99.9 % / Redundancy: 13.42 % / CC1/2: 0.99 / Rrim(I) all: 0.19 / Net I/σ(I): 12.84
Reflection shellResolution: 1.9→2.01 Å / Num. unique obs: 17476 / CC1/2: 0.61 / Rrim(I) all: 1.94

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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→48.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: FREE R-VALUE / ESU R: 0.148 / ESU R Free: 0.138
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2262 3302 3.001 %
Rwork0.1874 106743 -
all0.189 --
obs-110045 99.884 %
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: 30.528 Å2
Baniso -1Baniso -2Baniso -3
1-1.487 Å20 Å20 Å2
2--0.003 Å2-0 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9838 0 108 748 10694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01310280
X-RAY DIFFRACTIONr_bond_other_d0.0360.0179222
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.66314005
X-RAY DIFFRACTIONr_angle_other_deg2.3841.5821497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.44151307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36722.824517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.584151624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0751559
X-RAY DIFFRACTIONr_chiral_restr0.0660.21362
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211565
X-RAY DIFFRACTIONr_gen_planes_other0.010.022067
X-RAY DIFFRACTIONr_nbd_refined0.1990.21647
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.28508
X-RAY DIFFRACTIONr_nbtor_refined0.1580.24845
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.24379
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2534
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0990.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2220.224
X-RAY DIFFRACTIONr_nbd_other0.280.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2370.29
X-RAY DIFFRACTIONr_mcbond_it2.4173.115162
X-RAY DIFFRACTIONr_mcbond_other2.4163.1095161
X-RAY DIFFRACTIONr_mcangle_it3.4614.6426443
X-RAY DIFFRACTIONr_mcangle_other3.4614.6436444
X-RAY DIFFRACTIONr_scbond_it3.0733.4095118
X-RAY DIFFRACTIONr_scbond_other3.0723.4095119
X-RAY DIFFRACTIONr_scangle_it4.5524.9897546
X-RAY DIFFRACTIONr_scangle_other4.5524.9897547
X-RAY DIFFRACTIONr_lrange_it5.89336.03810749
X-RAY DIFFRACTIONr_lrange_other5.89236.04210750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9470.4032370.4127665X-RAY DIFFRACTION98.664
1.947-2.0010.2822370.2917643X-RAY DIFFRACTION99.9873
2.001-2.0590.2922280.277376X-RAY DIFFRACTION99.9869
2.059-2.1220.2862230.2587204X-RAY DIFFRACTION99.9865
2.122-2.1910.2722160.2316984X-RAY DIFFRACTION100
2.191-2.2680.2992080.2686737X-RAY DIFFRACTION99.9281
2.268-2.3530.2522030.2146557X-RAY DIFFRACTION100
2.353-2.4490.2321930.2026263X-RAY DIFFRACTION100
2.449-2.5580.2571870.196047X-RAY DIFFRACTION100
2.558-2.6820.2531790.185769X-RAY DIFFRACTION100
2.682-2.8270.231710.1725534X-RAY DIFFRACTION100
2.827-2.9980.2091620.1695237X-RAY DIFFRACTION100
2.998-3.2040.1971520.1714901X-RAY DIFFRACTION100
3.204-3.4590.2051420.1674615X-RAY DIFFRACTION100
3.459-3.7880.231310.1694237X-RAY DIFFRACTION100
3.788-4.2310.1841200.1413876X-RAY DIFFRACTION100
4.231-4.880.1611070.1253443X-RAY DIFFRACTION100
4.88-5.9620.188900.1482926X-RAY DIFFRACTION100
5.962-8.3680.173720.1692331X-RAY DIFFRACTION100
8.368-48.50.243440.1991398X-RAY DIFFRACTION99.7924

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