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- PDB-6y60: Structure of Human Polyomavirus 12 VP1 in complex with 3'-Sialyll... -

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Basic information

Entry
Database: PDB / ID: 6y60
TitleStructure of Human Polyomavirus 12 VP1 in complex with 3'-Sialyllactosamine
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
PHOSPHATE ION / N-acetyl-alpha-neuraminic acid / Capsid protein VP1
Similarity search - Component
Biological speciesHuman polyomavirus 12
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 12, 2020Group: Database references / Structure summary / Category: chem_comp / citation
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.2Jan 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
Revision 2.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)311,78925
Polymers307,08710
Non-polymers4,70315
Water32,8771825
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)156,05115
Polymers153,5435
Non-polymers2,50810
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25820 Å2
ΔGint-147 kcal/mol
Surface area44440 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)155,73810
Polymers153,5435
Non-polymers2,1955
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26650 Å2
ΔGint-152 kcal/mol
Surface area44320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.322, 141.724, 251.302
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Capsid protein VP1


Mass: 30708.664 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human polyomavirus 12 / Gene: VP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M4T5D3
#2: Polysaccharide
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-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/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1825 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium acetate, Bis-Tris, 2-methyl-2,4-pentanediol

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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: Jun 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.798→47.37 Å / Num. obs: 274251 / % possible obs: 99.4 % / Redundancy: 7.04 % / Biso Wilson estimate: 33.3 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.125 / Net I/σ(I): 12.21
Reflection shellResolution: 1.798→1.91 Å / Mean I/σ(I) obs: 1.34 / Num. unique obs: 42872 / CC1/2: 0.725 / Rrim(I) all: 1.77

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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: 1.798→47.37 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.699 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / ESU R: 0.127 / ESU R Free: 0.125
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.243 2741 1 %
Rwork0.2035 --
all0.204 --
obs-274154 99.412 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.486 Å2
Baniso -1Baniso -2Baniso -3
1-1.259 Å20 Å20 Å2
2--1.898 Å2-0 Å2
3----3.156 Å2
Refinement stepCycle: LAST / Resolution: 1.798→47.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19801 0 312 1825 21938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01320624
X-RAY DIFFRACTIONr_bond_other_d0.0010.01718085
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.67628223
X-RAY DIFFRACTIONr_angle_other_deg1.311.58142012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17552582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24622.417989
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.819153030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.35715115
X-RAY DIFFRACTIONr_chiral_restr0.0730.22796
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0223156
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024227
X-RAY DIFFRACTIONr_nbd_refined0.1990.23558
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.218752
X-RAY DIFFRACTIONr_nbtor_refined0.1620.29901
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.29090
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.21794
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0670.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2450.221
X-RAY DIFFRACTIONr_nbd_other0.2130.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.470.219
X-RAY DIFFRACTIONr_mcbond_it2.4223.22910355
X-RAY DIFFRACTIONr_mcbond_other2.4223.22910354
X-RAY DIFFRACTIONr_mcangle_it3.2174.83112928
X-RAY DIFFRACTIONr_mcangle_other3.2174.83112929
X-RAY DIFFRACTIONr_scbond_it2.7873.39810269
X-RAY DIFFRACTIONr_scbond_other2.7873.39810269
X-RAY DIFFRACTIONr_scangle_it3.9595.03115295
X-RAY DIFFRACTIONr_scangle_other3.9595.03115296
X-RAY DIFFRACTIONr_lrange_it5.2538.1622682
X-RAY DIFFRACTIONr_lrange_other5.1737.85422273
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
1.798-1.8440.4361890.376187720.377202250.3840.43393.75030.357
1.844-1.8950.341960.342194010.342196770.4880.49499.59340.307
1.895-1.9490.3491910.315189110.315191680.6540.67899.65570.273
1.949-2.0090.2921850.277183560.278185860.790.78399.75790.232
2.009-2.0750.3011800.268178510.268180660.7790.80499.80630.225
2.075-2.1480.2531750.239172730.239174740.8520.86199.85120.197
2.148-2.2290.2651680.224166840.225168660.870.87999.9170.184
2.229-2.320.2451630.204161300.205163000.910.91899.95710.168
2.32-2.4220.2311560.194154070.194155640.9180.93299.99360.157
2.422-2.540.2841490.2148010.201149580.8960.92699.94650.162
2.54-2.6770.2291420.196140560.196142040.9190.93199.95780.159
2.677-2.8390.2281350.193133570.193134990.9280.9399.94810.158
2.839-3.0340.2471270.188125540.189126850.9180.93899.96850.161
3.034-3.2760.2521190.185117270.185118480.9250.9499.98310.164
3.276-3.5870.2461090.181108350.181109480.9290.94899.96350.167
3.587-4.0080.21990.17298290.17299320.9470.95699.95970.164
4.008-4.6220.172880.14887300.14988180.9660.9711000.148
4.622-5.6480.178760.15674330.15675170.9630.9799.89360.157
5.648-7.9310.229590.20458500.20559130.9410.94699.93240.203
7.931-47.370.254350.2234560.22135060.950.93899.57220.232

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