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- PDB-6y5y: Structure of New Jersey Polyomavirus VP1 in complex with 3'-Sialy... -

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Basic information

Entry
Database: PDB / ID: 6y5y
TitleStructure of New Jersey Polyomavirus VP1 in complex with 3'-Sialyllactose
ComponentsVP1
KeywordsVIRAL PROTEIN / Major Capsid Protein / Polyomavirus
Function / homologyCapsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid / viral capsid / structural molecule activity / 3'-sialyl-alpha-lactose / VP1
Function and homology information
Biological speciesNew Jersey polyomavirus-2013
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 22, 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 / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
A: VP1
B: VP1
C: VP1
D: VP1
E: VP1
F: VP1
G: VP1
H: VP1
I: VP1
J: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)351,13669
Polymers340,96610
Non-polymers10,17059
Water50,0282777
1
A: VP1
B: VP1
C: VP1
D: VP1
E: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,70636
Polymers170,4835
Non-polymers5,22331
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32900 Å2
ΔGint-171 kcal/mol
Surface area50220 Å2
MethodPISA
2
F: VP1
G: VP1
H: VP1
I: VP1
J: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,43033
Polymers170,4835
Non-polymers4,94728
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31270 Å2
ΔGint-166 kcal/mol
Surface area49450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.381, 151.082, 130.617
Angle α, β, γ (deg.)90.000, 106.561, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
VP1


Mass: 34096.566 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) New Jersey polyomavirus-2013 / Gene: VP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta 2 / References: UniProt: A0A024B5J2

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Sugars , 2 types, 10 molecules

#2: Polysaccharide
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / 3'-sialyl-alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 633.552 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-alpha-lactose
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Polysaccharide
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 633.552 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpb1-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_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 2826 molecules

#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2777 / 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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Succinic acid, PEG 3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2014
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.8→48.2 Å / Num. obs: 295112 / % possible obs: 99.83 % / Redundancy: 5.7 % / Biso Wilson estimate: 19.03 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.1556 / Net I/σ(I): 9.79
Reflection shellResolution: 1.801→1.865 Å / Mean I/σ(I) obs: 1.39 / Num. unique obs: 29218 / CC1/2: 0.603 / Rrim(I) all: 1.176

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FMG

4fmg


Resolution: 1.8→48.2 Å / SU ML: 0.2213 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.455
RfactorNum. reflection% reflection
Rfree0.2064 5902 2 %
Rwork0.166 --
obs0.1668 295026 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.67 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21240 0 674 2777 24691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006422744
X-RAY DIFFRACTIONf_angle_d0.851630961
X-RAY DIFFRACTIONf_chiral_restr0.05583465
X-RAY DIFFRACTIONf_plane_restr0.00554020
X-RAY DIFFRACTIONf_dihedral_angle_d3.835819015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.341910.31369320X-RAY DIFFRACTION96.78
1.82-1.840.35681970.29129663X-RAY DIFFRACTION99.98
1.84-1.870.31241960.27389583X-RAY DIFFRACTION99.91
1.87-1.890.2971960.25819642X-RAY DIFFRACTION99.92
1.89-1.910.26881970.2429649X-RAY DIFFRACTION99.95
1.91-1.940.25671960.22689560X-RAY DIFFRACTION99.87
1.94-1.970.25841960.21349617X-RAY DIFFRACTION99.95
1.97-20.22911960.20229623X-RAY DIFFRACTION99.92
2-2.030.22231970.19719636X-RAY DIFFRACTION99.94
2.03-2.060.23021970.1989617X-RAY DIFFRACTION99.94
2.06-2.10.24511970.1939679X-RAY DIFFRACTION99.92
2.1-2.140.24621960.1889591X-RAY DIFFRACTION99.93
2.14-2.180.21781970.17699656X-RAY DIFFRACTION99.94
2.18-2.220.23071970.17779664X-RAY DIFFRACTION99.89
2.22-2.270.23761970.17499619X-RAY DIFFRACTION99.88
2.27-2.320.22991960.17389643X-RAY DIFFRACTION99.82
2.32-2.380.22471960.17149603X-RAY DIFFRACTION99.95
2.38-2.440.22821970.16979618X-RAY DIFFRACTION99.95
2.44-2.520.21881970.16439678X-RAY DIFFRACTION99.99
2.52-2.60.19261970.16569644X-RAY DIFFRACTION99.95
2.6-2.690.23661970.16199636X-RAY DIFFRACTION99.93
2.69-2.80.1981970.15999685X-RAY DIFFRACTION99.94
2.8-2.920.19331970.15669633X-RAY DIFFRACTION99.97
2.92-3.080.21431970.16039638X-RAY DIFFRACTION99.82
3.08-3.270.20821970.15229673X-RAY DIFFRACTION99.86
3.27-3.520.17561970.14419646X-RAY DIFFRACTION99.93
3.52-3.880.17641980.13639696X-RAY DIFFRACTION99.95
3.88-4.440.14151980.11679681X-RAY DIFFRACTION99.98
4.44-5.590.14811980.12549736X-RAY DIFFRACTION99.95
5.59-48.20.18582000.15919795X-RAY DIFFRACTION99.59

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