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- PDB-6y64: Structure of Sheep Polyomavirus VP1 in complex with 6'-Sialyllact... -

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Basic information

Entry
Database: PDB / ID: 6y64
TitleStructure of Sheep Polyomavirus VP1 in complex with 6'-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 / metal ion binding
Similarity search - Function
Capsid protein VP1,Polyomavirus / Polyomavirus Vp1; Chain A / Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid / Sandwich / Mainly Beta
Similarity search - Domain/homology
6'-sialyl-N-acetyllactosamine / N-acetyl-alpha-neuraminic acid / Capsid protein VP1
Similarity search - Component
Biological speciesSheep polyomavirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_validate_close_contact / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.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 / _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_alt_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_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_alt_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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
E: Capsid protein VP1
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
J: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,29962
Polymers324,66510
Non-polymers5,63452
Water49,5952753
1
A: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
E: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,64728
Polymers162,3335
Non-polymers2,31523
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28500 Å2
ΔGint-199 kcal/mol
Surface area43440 Å2
MethodPISA
2
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
J: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,65234
Polymers162,3335
Non-polymers3,31929
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30160 Å2
ΔGint-210 kcal/mol
Surface area44110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.620, 81.260, 146.660
Angle α, β, γ (deg.)90.00, 115.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
Capsid protein VP1


Mass: 32466.500 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, 6 molecules

#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-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/a6-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 6'-sialyl-N-acetyllactosamine


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b6-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#7: 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.: 2
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

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Non-polymers , 4 types, 2799 molecules

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


Mass: 92.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2753 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Magnesium chloride, PEG 800, TRIS

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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: Nov 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→47.47 Å / Num. obs: 350203 / % possible obs: 96.81 % / Redundancy: 6.8 % / Biso Wilson estimate: 17.04 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.071 / Net I/σ(I): 17.78
Reflection shellResolution: 1.6→1.657 Å / Mean I/σ(I) obs: 2.94 / Num. unique obs: 34182 / CC1/2: 0.821 / Rrim(I) all: 0.727

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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: 1.6→47.47 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.052 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.076 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18218 3503 1 %RANDOM
Rwork0.15167 ---
obs0.15197 346733 96.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å2-0.46 Å2
2--0.34 Å20 Å2
3---0.56 Å2
Refinement stepCycle: 1 / Resolution: 1.6→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19623 0 366 2753 22742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01320654
X-RAY DIFFRACTIONr_bond_other_d0.0010.01718371
X-RAY DIFFRACTIONr_angle_refined_deg1.511.66828066
X-RAY DIFFRACTIONr_angle_other_deg1.4061.57942702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.23852579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91322.5341026
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.426153116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.77115109
X-RAY DIFFRACTIONr_chiral_restr0.0740.22700
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0223228
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024426
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.911.4710241
X-RAY DIFFRACTIONr_mcbond_other0.9091.4710240
X-RAY DIFFRACTIONr_mcangle_it1.5452.19712809
X-RAY DIFFRACTIONr_mcangle_other1.5452.19712810
X-RAY DIFFRACTIONr_scbond_it1.1431.6210413
X-RAY DIFFRACTIONr_scbond_other1.1431.6210414
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8132.37215246
X-RAY DIFFRACTIONr_long_range_B_refined4.63118.91523034
X-RAY DIFFRACTIONr_long_range_B_other4.63118.91523035
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 252 -
Rwork0.225 24981 -
obs--94.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.154-0.0309-0.00480.2378-0.01990.0342-0.00650.00640.03970.0880.0056-0.0498-0.0191-0.03080.00090.04570.0066-0.01740.03440.00180.0182-18.95111.607-14.516
20.14720.0339-0.00510.2609-0.03610.081-0.00840.04180.0283-0.02410.0036-0.0579-0.0306-0.03110.00490.0230.00590.00460.03140.01210.0224-15.55413.237-42.56
30.13540.02660.07020.32710.02410.06920.00480.0097-0.0288-0.111-0.0011-0.08790.0071-0.0336-0.00370.0416-0.00920.0310.0505-0.01550.0331-14.523-12.914-53.257
40.09360.0195-0.0460.237-0.03950.082-0.0140.0005-0.0483-0.0027-0.0036-0.07370.0295-0.03940.01760.0136-0.0151-0.00260.02980.00770.0539-14.992-30.825-31.321
50.1878-0.0038-0.06210.149-0.00930.0491-0.0057-0.024-0.01590.09970.0091-0.04680.0058-0.0216-0.00340.0712-0.0053-0.03620.03530.01370.0234-19.086-16.098-7.42
60.1307-0.0430.04340.2546-0.02610.0601-0.0016-0.0058-0.04480.12670.02180.0715-0.00420.0341-0.02020.06650.01250.03010.03240.00470.029-82.868-16.557-13.412
70.0489-0.0181-0.02290.22110.00150.0568-0.0074-0.0001-0.02870.01290.00490.03990.02990.02790.00240.02610.0128-0.00460.0198-0.00060.0338-81.557-33.283-36.144
80.10260.0119-0.0140.08510.00190.0596-0.00470.0130.0046-0.05280.00530.02860.01840.0248-0.00060.03990.0067-0.01870.0205-0.00770.0218-78.304-17.309-59.289
90.0735-0.0095-0.01060.2229-0.03150.02410.0158-0.0090.0188-0.0434-0.0110.0462-0.00910.0222-0.00470.0308-0.0067-0.00380.02690.00350.022-80.6049.905-51.072
100.1492-0.04310.02650.2531-0.00040.1238-0.0039-0.01440.00930.08460.0220.0672-0.05020.0373-0.01820.0518-0.01070.03360.0158-0.00310.0251-83.729.987-22.969
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 402
2X-RAY DIFFRACTION2B34 - 401
3X-RAY DIFFRACTION3C34 - 401
4X-RAY DIFFRACTION4D34 - 402
5X-RAY DIFFRACTION5E33 - 402
6X-RAY DIFFRACTION6F33 - 402
7X-RAY DIFFRACTION7G33 - 403
8X-RAY DIFFRACTION8H34 - 402
9X-RAY DIFFRACTION9I34 - 403
10X-RAY DIFFRACTION10J34 - 403

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