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- PDB-7b6v: Sheep Polyomavirus VP1 in complex with 5 mM Forssman antigen pent... -

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Basic information

Entry
Database: PDB / ID: 7b6v
TitleSheep Polyomavirus VP1 in complex with 5 mM Forssman antigen pentaose and 20 mM 3'-sialyllactosamine
ComponentsCapsid protein VP1
KeywordsVIRAL PROTEIN / polyomavirus / capsid protein / VP1 / glycan complex
Function / homology
Function and homology information


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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / N-acetyl-alpha-neuraminic acid / Capsid protein VP1
Similarity search - Component
Biological speciesSheep polyomavirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsRustmeier, N.H. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2327 Germany
CitationJournal: Biorxiv / Year: 2023
Title: A novel and highly specific Forssman antigen-binding protein from sheep polyomavirus
Authors: Rustmeier, N.H. / Silva, L.M. / Di Maio, A. / Mueller, J.C. / Herrmann, A. / Feizi, T. / Liu, Y. / Stehle, T.
History
DepositionDec 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Feb 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: Capsid protein VP1
BBB: Capsid protein VP1
CCC: Capsid protein VP1
DDD: Capsid protein VP1
EEE: Capsid protein VP1
FFF: Capsid protein VP1
GGG: Capsid protein VP1
HHH: Capsid protein VP1
III: Capsid protein VP1
JJJ: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)315,65540
Polymers305,77410
Non-polymers9,88130
Water42,3712352
1
AAA: Capsid protein VP1
BBB: Capsid protein VP1
CCC: Capsid protein VP1
DDD: Capsid protein VP1
EEE: Capsid protein VP1
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 158 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)157,65719
Polymers152,8875
Non-polymers4,77014
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
FFF: Capsid protein VP1
GGG: Capsid protein VP1
HHH: Capsid protein VP1
III: Capsid protein VP1
JJJ: Capsid protein VP1
hetero molecules


  • defined by author
  • 158 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)157,99821
Polymers152,8875
Non-polymers5,11116
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.404, 130.404, 221.221
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 10 molecules AAABBBCCCDDDEEEFFFGGGHHHIIIJJJ

#1: Protein
Capsid protein VP1 /


Mass: 30577.434 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sheep polyomavirus 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E3ZCF3

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Sugars , 3 types, 15 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)- ...2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpNAca1-3DGalpNAcb1-3DGalpa1-4DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2112h-1b_1-5][a2112h-1a_1-5][a2112h-1b_1-5_2*NCC/3=O][a2112h-1a_1-5_2*NCC/3=O]/1-2-3-4/a4-b1_b3-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(4+1)][a-D-Galp]{[(3+1)][b-D-GalpNAc]{[(3+1)][a-D-GalpNAc]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)- ...2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpNAca1-3DGalpNAcb1-3DGalpa1-4DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,5,4/[a2122h-1b_1-5][a2112h-1b_1-5][a2112h-1a_1-5][a2112h-1b_1-5_2*NCC/3=O][a2112h-1a_1-5_2*NCC/3=O]/1-2-3-4-5/a4-b1_b4-c1_c3-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(4+1)][a-D-Galp]{[(3+1)][b-D-GalpNAc]{[(3+1)][a-D-GalpNAc]{}}}}}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.: 5 / 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 , 5 types, 2367 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 2352 / 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: 3.55 Å3/Da / Density % sol: 65.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: KSCN, PEG 3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.6413
pseudo-merohedral22K, H, -L20.3587
ReflectionResolution: 1.798→48.85 Å / Num. obs: 390469 / % possible obs: 99.8 % / Redundancy: 9.9 % / Biso Wilson estimate: 28.5 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.162 / Net I/σ(I): 11.02
Reflection shellResolution: 1.8→1.91 Å / Mean I/σ(I) obs: 1.51 / Num. unique obs: 62546 / CC1/2: 0.471 / Rrim(I) all: 1.273

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y61

6y61


Resolution: 1.798→48.846 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.168 / WRfactor Rwork: 0.146 / Average fsc free: 0.9726 / Average fsc work: 0.9809 / Cross valid method: FREE R-VALUE / ESU R: 0.017 / ESU R Free: 0.017
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.177 6588 1.687 %
Rwork0.1521 383851 -
all0.153 --
obs-390439 99.8 %
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: 24.646 Å2
Baniso -1Baniso -2Baniso -3
1-0.211 Å20 Å20 Å2
2--0.211 Å20 Å2
3----0.421 Å2
Refinement stepCycle: LAST / Resolution: 1.798→48.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20301 0 665 2352 23318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01321515
X-RAY DIFFRACTIONr_bond_other_d0.0350.01719040
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.69829294
X-RAY DIFFRACTIONr_angle_other_deg2.8611.60644326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.93252615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66322.4161068
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.888153182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.19815120
X-RAY DIFFRACTIONr_chiral_restr0.0790.22940
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0223820
X-RAY DIFFRACTIONr_gen_planes_other0.0140.024561
X-RAY DIFFRACTIONr_nbd_refined0.1830.23744
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.219038
X-RAY DIFFRACTIONr_nbtor_refined0.1660.210254
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0970.29122
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.21902
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0680.27
X-RAY DIFFRACTIONr_metal_ion_refined0.1520.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1210.226
X-RAY DIFFRACTIONr_nbd_other0.2760.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.248
X-RAY DIFFRACTIONr_mcbond_it2.0362.55910517
X-RAY DIFFRACTIONr_mcbond_other2.0362.55810516
X-RAY DIFFRACTIONr_mcangle_it2.7643.82613107
X-RAY DIFFRACTIONr_mcangle_other2.7633.82613108
X-RAY DIFFRACTIONr_scbond_it2.1532.67610998
X-RAY DIFFRACTIONr_scbond_other2.1532.67610999
X-RAY DIFFRACTIONr_scangle_it2.9693.96716185
X-RAY DIFFRACTIONr_scangle_other2.9693.96716186
X-RAY DIFFRACTIONr_lrange_it4.51230.26223555
X-RAY DIFFRACTIONr_lrange_other4.36229.88923073
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.798-1.8450.264720.16727716X-RAY DIFFRACTION97.4352
1.845-1.8950.2594540.21927724X-RAY DIFFRACTION100
1.895-1.950.3364710.28726958X-RAY DIFFRACTION99.9308
1.95-2.010.2034430.1526144X-RAY DIFFRACTION100
2.01-2.0760.2364400.20825308X-RAY DIFFRACTION99.9534
2.076-2.1480.1864010.15724593X-RAY DIFFRACTION100
2.148-2.2290.1783730.1523665X-RAY DIFFRACTION100
2.229-2.320.2133790.17522778X-RAY DIFFRACTION99.9655
2.32-2.4230.183810.13721930X-RAY DIFFRACTION100
2.423-2.5410.1663720.13220870X-RAY DIFFRACTION100
2.541-2.6780.1743320.13619865X-RAY DIFFRACTION100
2.678-2.840.1643570.13618746X-RAY DIFFRACTION100
2.84-3.0350.1752900.14617710X-RAY DIFFRACTION100
3.035-3.2780.1592950.14816376X-RAY DIFFRACTION100
3.278-3.5890.1612650.15115133X-RAY DIFFRACTION100
3.589-4.010.1572440.13613735X-RAY DIFFRACTION100
4.01-4.6250.1082190.11312020X-RAY DIFFRACTION100
4.625-5.6520.1391780.13110236X-RAY DIFFRACTION100
5.652-7.940.1871360.1657884X-RAY DIFFRACTION100
7.94-48.8460.211860.174460X-RAY DIFFRACTION99.978

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