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- PDB-7zio: JC Polyomavirus VP1 in complex with 6'-Sialyllactose glycomacromo... -

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Basic information

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


T=7 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / 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
6'-sialyl-lactose / DI(HYDROXYETHYL)ETHER / Major capsid protein VP1
Similarity search - Component
Biological speciesJC polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.751 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: 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)152,91020
Polymers150,3795
Non-polymers2,53115
Water27,4731525
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27610 Å2
ΔGint-118 kcal/mol
Surface area47010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.020, 97.258, 129.075
Angle α, β, γ (deg.)90.000, 110.298, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 5 molecules AAABBBCCCDDDEEE

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


Mass: 30075.861 Da / Num. of mol.: 5 / Fragment: UNP residues 23-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) JC polyomavirus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03089

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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, Oligosaccharide / Class: Nutrient / Mass: 633.552 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6'-sialyl-lactose
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
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6'-sialyl-lactose
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[][a-D-Neup5Ac]{}LINUCSPDB-CARE

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Non-polymers , 5 types, 1537 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1525 / 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: 2.94 Å3/Da / Density % sol: 58.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 0.2 M KSCN, 12% (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: 1.75→45.165 Å / Num. obs: 173290 / % possible obs: 99.2 % / Redundancy: 5.07 % / CC1/2: 0.99 / Rrim(I) all: 0.18 / Net I/σ(I): 8.31
Reflection shellResolution: 1.75→1.86 Å / Num. unique obs: 27318 / CC1/2: 0.58 / 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: 3NXD

3nxd


Resolution: 1.751→45.165 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.075 / SU ML: 0.089 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.101
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2168 3466 2 %
Rwork0.1828 169812 -
all0.184 --
obs-173278 99.294 %
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: 19.461 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å2-0.487 Å2
2--1.054 Å20 Å2
3----0.639 Å2
Refinement stepCycle: LAST / Resolution: 1.751→45.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10058 0 146 1525 11729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01310616
X-RAY DIFFRACTIONr_bond_other_d0.0040.0179527
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.66414451
X-RAY DIFFRACTIONr_angle_other_deg1.381.58222202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.28351340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94222.678549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.879151702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2621564
X-RAY DIFFRACTIONr_chiral_restr0.0760.21401
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211938
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022189
X-RAY DIFFRACTIONr_nbd_refined0.20.21728
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.28653
X-RAY DIFFRACTIONr_nbtor_refined0.1590.24992
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.24289
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.21069
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1690.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1350.28
X-RAY DIFFRACTIONr_nbd_other0.180.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.218
X-RAY DIFFRACTIONr_mcbond_it1.3711.8365266
X-RAY DIFFRACTIONr_mcbond_other1.3691.8365265
X-RAY DIFFRACTIONr_mcangle_it2.0192.746589
X-RAY DIFFRACTIONr_mcangle_other2.022.7416590
X-RAY DIFFRACTIONr_scbond_it2.1042.1075350
X-RAY DIFFRACTIONr_scbond_other2.1032.1075351
X-RAY DIFFRACTIONr_scangle_it3.2883.0547846
X-RAY DIFFRACTIONr_scangle_other3.2873.0547847
X-RAY DIFFRACTIONr_lrange_it5.36523.36911703
X-RAY DIFFRACTIONr_lrange_other4.98322.32611262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.751-1.7970.4672410.41511811X-RAY DIFFRACTION93.8849
1.797-1.8460.3442500.32312263X-RAY DIFFRACTION99.9601
1.846-1.90.3122450.28511996X-RAY DIFFRACTION99.951
1.9-1.9580.382340.36811480X-RAY DIFFRACTION99.406
1.958-2.0220.2412310.20711280X-RAY DIFFRACTION99.9479
2.022-2.0930.2432210.22710836X-RAY DIFFRACTION99.7024
2.093-2.1720.2152140.17710496X-RAY DIFFRACTION99.8695
2.172-2.2610.2582060.21710076X-RAY DIFFRACTION99.5546
2.261-2.3610.231970.1939661X-RAY DIFFRACTION99.225
2.361-2.4760.2081880.1519233X-RAY DIFFRACTION99.7142
2.476-2.610.1781800.1418836X-RAY DIFFRACTION99.7566
2.61-2.7690.1821700.1468326X-RAY DIFFRACTION99.5664
2.769-2.960.1871600.1417822X-RAY DIFFRACTION99.7625
2.96-3.1970.1881500.1467350X-RAY DIFFRACTION99.9201
3.197-3.5010.1761370.1476727X-RAY DIFFRACTION99.8545
3.501-3.9140.21250.1476085X-RAY DIFFRACTION99.4077
3.914-4.5190.1461090.125368X-RAY DIFFRACTION99.745
4.519-5.5330.165940.1454597X-RAY DIFFRACTION99.9148
5.533-7.8160.251730.2113564X-RAY DIFFRACTION100
7.816-45.1650.226410.2112005X-RAY DIFFRACTION99.3204

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