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- PDB-6y65: Structure of apo Goose Hemorrhagic Polyomavirus VP1 -

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Basic information

Entry
Database: PDB / ID: 6y65
TitleStructure of apo Goose Hemorrhagic Polyomavirus VP1
ComponentsCapsid protein VP1
KeywordsVIRAL PROTEIN / Major Capsid Protein / Polyomavirus
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
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
IMIDAZOLE / Capsid protein VP1
Similarity search - Component
Biological speciesGoose hemorrhagic polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsStroh, L.J. / Rustmeier, N.H. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2327 Germany
CitationJournal: Mbio / Year: 2020
Title: Structural Basis and Evolution of Glycan Receptor Specificities within the Polyomavirus Family.
Authors: Stroh, L.J. / Rustmeier, N.H. / Blaum, B.S. / Botsch, J. / Rossler, P. / Wedekink, F. / Lipkin, W.I. / Mishra, N. / Stehle, T.
History
DepositionFeb 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)318,644130
Polymers311,61310
Non-polymers7,031120
Water59,2513289
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)159,46367
Polymers155,8075
Non-polymers3,65662
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32100 Å2
ΔGint-60 kcal/mol
Surface area46460 Å2
MethodPISA
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)159,18163
Polymers155,8075
Non-polymers3,37458
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30990 Å2
ΔGint-87 kcal/mol
Surface area46200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.290, 90.410, 100.840
Angle α, β, γ (deg.)94.048, 97.898, 108.064
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Capsid protein VP1


Mass: 31161.332 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Goose hemorrhagic polyomavirus / Gene: VP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q80FI3
#2: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 98 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3289 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Na nitrate, Na phosphate dibasic, ammonium sulfate, MES, imidazole, PEG 8000, ethylene glycol

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→45.97 Å / Num. obs: 487522 / % possible obs: 95.36 % / Redundancy: 3.6 % / Biso Wilson estimate: 12.8 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.068 / Net I/σ(I): 14.26
Reflection shellResolution: 1.45→1.502 Å / Mean I/σ(I) obs: 2.16 / Num. unique obs: 46392 / CC1/2: 0.797 / Rrim(I) all: 0.702

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FMG

4fmg


Resolution: 1.45→45.97 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.992 / SU ML: 0.038 / Cross valid method: FREE R-VALUE / ESU R: 0.055 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1703 4875 1 %
Rwork0.1484 --
all0.149 --
obs-487470 95.379 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.236 Å2
Baniso -1Baniso -2Baniso -3
1-0.648 Å2-0.208 Å2-0.707 Å2
2--0.117 Å2-0.675 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.45→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20009 0 434 3289 23732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01321514
X-RAY DIFFRACTIONr_bond_other_d0.0020.01719699
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.66329303
X-RAY DIFFRACTIONr_angle_other_deg1.4211.56545865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.58152833
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.99521.981949
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.905153277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.13615130
X-RAY DIFFRACTIONr_chiral_restr0.0780.22779
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0224500
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024306
X-RAY DIFFRACTIONr_nbd_refined0.1950.23400
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.218887
X-RAY DIFFRACTIONr_nbtor_refined0.1630.210266
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.29885
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.22508
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1480.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3060.223
X-RAY DIFFRACTIONr_nbd_other0.2080.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1190.225
X-RAY DIFFRACTIONr_mcbond_it0.8621.20811039
X-RAY DIFFRACTIONr_mcbond_other0.8611.20811038
X-RAY DIFFRACTIONr_mcangle_it1.4021.80813925
X-RAY DIFFRACTIONr_mcangle_other1.4021.80813926
X-RAY DIFFRACTIONr_scbond_it1.2171.36610475
X-RAY DIFFRACTIONr_scbond_other1.2171.36710476
X-RAY DIFFRACTIONr_scangle_it1.8471.96415363
X-RAY DIFFRACTIONr_scangle_other1.8471.96515364
X-RAY DIFFRACTIONr_lrange_it4.57816.2323878
X-RAY DIFFRACTIONr_lrange_other4.57816.23223879
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.45-1.4880.2693410.237338200.237377690.8870.89790.44720.237
1.488-1.5280.2523410.222337020.222369030.90.90792.250.222
1.528-1.5730.2083340.198331160.198357620.9340.93793.5350.198
1.573-1.6210.2123280.189324040.189347580.9360.93994.17110.189
1.621-1.6740.2143200.181317570.182338700.9310.93994.70620.181
1.674-1.7330.2023100.172306200.173325350.9360.94595.06680.172
1.733-1.7980.1893000.158296950.158314420.950.95895.39790.158
1.798-1.8710.1642900.148287210.148302830.960.96595.79960.148
1.871-1.9540.1792780.146275800.146289810.9590.96696.1250.146
1.954-2.050.1542690.137265700.137278020.9680.97296.53620.137
2.05-2.160.1572550.139253050.139263770.9670.9796.90260.139
2.16-2.2910.1582430.14240510.14250550.9540.96196.96270.14
2.291-2.4490.1562280.127225540.128234180.9680.97497.28410.127
2.449-2.6440.1462130.129210820.129218610.9730.97497.41090.129
2.644-2.8960.1381960.13193790.13200880.9720.97397.44620.13
2.896-3.2360.1781760.133174810.134182440.9590.97196.78250.133
3.236-3.7330.1551560.141153750.141160280.9690.97396.89920.141
3.733-4.5650.1561340.126132880.126135360.970.97699.15780.126
4.565-6.4240.1741040.15103250.15104880.980.98199.43750.15
6.424-45.960.147590.1757710.1758740.9760.96999.25090.17

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