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- PDB-7b6t: Sheep Polyomavirus VP1 in complex with 10 mM globo-N-tetraose -

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Basic information

Entry
Database: PDB / ID: 7b6t
TitleSheep Polyomavirus VP1 in complex with 10 mM globo-N-tetraose
ComponentsCapsid protein VP1
KeywordsVIRAL PROTEIN / polyomavirus / capsid protein / VP1 / glycan complex
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / metal ion binding
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 / Capsid protein VP1
Similarity search - Component
Biological speciesSheep polyomavirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 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)312,30968
Polymers305,77410
Non-polymers6,53558
Water57,7023203
1
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)156,53434
Polymers152,8875
Non-polymers3,64629
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


Theoretical massNumber of molelcules
Total (without water)155,77534
Polymers152,8875
Non-polymers2,88829
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.274, 130.274, 222.145
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 , 2 types, 7 molecules

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


Type: oligosaccharide / Mass: 545.490 Da / Num. of mol.: 4 / Source method: isolated from a natural source
DescriptorTypeProgram
DGalpNAcb1-3DGalpa1-4DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1b_1-5][a2112h-1a_1-5][a2112h-1b_1-5_2*NCC/3=O]/1-2-3/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(4+1)][a-D-Galp]{[(3+1)][b-D-GalpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
DGalpNAcb1-3DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5][a2112h-1b_1-5_2*NCC/3=O]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{[(3+1)][b-D-GalpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 7 types, 3254 molecules

#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: Mg
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: K
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3203 / 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: 3.56 Å3/Da / Density % sol: 65.44 %
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: Dec 13, 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, L10.7916
pseudo-merohedral22K, H, -L20.2084
ReflectionResolution: 1.7→48.91 Å / Num. obs: 462792 / % possible obs: 99.9 % / Redundancy: 5.78 % / Biso Wilson estimate: 27.9 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.107 / Net I/σ(I): 13.51
Reflection shellResolution: 1.7→1.8 Å / Mean I/σ(I) obs: 1.61 / Num. unique obs: 74733 / CC1/2: 0.485 / Rrim(I) all: 1.085

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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: 1.701→48.908 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / Cross valid method: FREE R-VALUE / ESU R: 0.014 / ESU R Free: 0.014
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1651 4550 1 %
Rwork0.1433 458240 -
all0.144 --
obs-458240 99.951 %
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: 22.373 Å2
Baniso -1Baniso -2Baniso -3
1--2.032 Å2-0 Å2-0 Å2
2---2.032 Å2-0 Å2
3---4.065 Å2
Refinement stepCycle: LAST / Resolution: 1.701→48.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20328 0 411 3203 23942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01321230
X-RAY DIFFRACTIONr_bond_other_d0.0360.01718986
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.67328831
X-RAY DIFFRACTIONr_angle_other_deg2.5431.58244068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.44652630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19522.3331046
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.507153169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.06115118
X-RAY DIFFRACTIONr_chiral_restr0.0790.22826
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0223718
X-RAY DIFFRACTIONr_gen_planes_other0.0150.024527
X-RAY DIFFRACTIONr_nbd_refined0.20.23707
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.218346
X-RAY DIFFRACTIONr_nbtor_refined0.1680.210139
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.29230
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.22300
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0720.25
X-RAY DIFFRACTIONr_metal_ion_refined0.2750.215
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1850.215
X-RAY DIFFRACTIONr_nbd_other0.2720.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.272
X-RAY DIFFRACTIONr_mcbond_it1.7272.20410568
X-RAY DIFFRACTIONr_mcbond_other1.7272.20410567
X-RAY DIFFRACTIONr_mcangle_it2.4933.29713176
X-RAY DIFFRACTIONr_mcangle_other2.4933.29713177
X-RAY DIFFRACTIONr_scbond_it2.0872.39110662
X-RAY DIFFRACTIONr_scbond_other2.0862.39110663
X-RAY DIFFRACTIONr_scangle_it2.9833.51115653
X-RAY DIFFRACTIONr_scangle_other2.9833.51215654
X-RAY DIFFRACTIONr_lrange_it5.15327.53123849
X-RAY DIFFRACTIONr_lrange_other4.85426.57823009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.701-1.7450.2633350.22633647X-RAY DIFFRACTION99.4149
1.745-1.7930.253620.20233030X-RAY DIFFRACTION99.994
1.793-1.8450.232950.18832110X-RAY DIFFRACTION100
1.845-1.9020.2142970.17131240X-RAY DIFFRACTION100
1.902-1.9640.1843060.16830219X-RAY DIFFRACTION99.9967
1.964-2.0330.1722740.15729324X-RAY DIFFRACTION100
2.033-2.1090.172950.14628189X-RAY DIFFRACTION99.9965
2.109-2.1950.1622600.14327154X-RAY DIFFRACTION99.9964
2.195-2.2930.1712530.14126095X-RAY DIFFRACTION100
2.293-2.4040.1562460.13424875X-RAY DIFFRACTION99.996
2.404-2.5340.172470.13423678X-RAY DIFFRACTION100
2.534-2.6870.1432130.13722413X-RAY DIFFRACTION100
2.687-2.8720.1642150.13221053X-RAY DIFFRACTION100
2.872-3.1010.1531980.13419617X-RAY DIFFRACTION99.9849
3.101-3.3960.1591830.14217965X-RAY DIFFRACTION99.9835
3.396-3.7950.1551610.13816351X-RAY DIFFRACTION99.9879
3.795-4.3770.1271480.11314374X-RAY DIFFRACTION100
4.377-5.350.1211180.11312211X-RAY DIFFRACTION100
5.35-7.5220.165960.1539417X-RAY DIFFRACTION100
7.522-48.9080.224480.1755278X-RAY DIFFRACTION99.7565

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