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- PDB-6esb: BK polyomavirus + 20 mM GT1b oligosaccharide -

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Basic information

Entry
Database: PDB / ID: 6esb
TitleBK polyomavirus + 20 mM GT1b oligosaccharide
Components
  • Capsid protein VP1
  • Minor capsid protein VP2
KeywordsVIRUS / Polyomavirus / Receptor / Complex / Glycan
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / symbiont entry into host cell via permeabilization of host membrane / T=7 icosahedral viral capsid / viral penetration into host nucleus / viral capsid / host cell / channel activity / monoatomic ion transmembrane transport / host cell endoplasmic reticulum membrane / endocytosis involved in viral entry into host cell ...caveolin-mediated endocytosis of virus by host cell / symbiont entry into host cell via permeabilization of host membrane / T=7 icosahedral viral capsid / viral penetration into host nucleus / viral capsid / host cell / channel activity / monoatomic ion transmembrane transport / host cell endoplasmic reticulum membrane / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / DNA binding / membrane
Similarity search - Function
Polyomavirus coat protein VP2 / Polyomavirus coat protein / 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
Major capsid protein VP1 / Minor capsid protein VP2 / Capsid protein VP1
Similarity search - Component
Biological speciesBK polyomavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsHurdiss, D.L. / Ranson, N.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust102572/B/13/Z United Kingdom
CitationJournal: Structure / Year: 2018
Title: The Structure of an Infectious Human Polyomavirus and Its Interactions with Cellular Receptors.
Authors: Daniel L Hurdiss / Martin Frank / Joseph S Snowden / Andrew Macdonald / Neil A Ranson /
Abstract: BK polyomavirus (BKV) causes polyomavirus-associated nephropathy and hemorrhagic cystitis in immunosuppressed patients. These are diseases for which we currently have limited treatment options, but ...BK polyomavirus (BKV) causes polyomavirus-associated nephropathy and hemorrhagic cystitis in immunosuppressed patients. These are diseases for which we currently have limited treatment options, but potential therapies could include pre-transplant vaccination with a multivalent BKV vaccine or therapeutics which inhibit capsid assembly or block attachment and entry into target cells. A useful tool in such efforts would be a high-resolution structure of the infectious BKV virion and how this interacts with its full repertoire of cellular receptors. We present the 3.4-Å cryoelectron microscopy structure of native, infectious BKV in complex with the receptor fragment of GT1b ganglioside. We also present structural evidence that BKV can utilize glycosaminoglycans as attachment receptors. This work highlights features that underpin capsid stability and provides a platform for rational design and development of urgently needed pharmacological interventions for BKV-associated diseases.
History
DepositionOct 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _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.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 2.1May 15, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-3944
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  • Superimposition on EM map
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Capsid protein VP1
2: Capsid protein VP1
3: Capsid protein VP1
4: Capsid protein VP1
5: Capsid protein VP1
6: Capsid protein VP1
7: Minor capsid protein VP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,41719
Polymers278,5737
Non-polymers3,84412
Water00
1
1: Capsid protein VP1
2: Capsid protein VP1
3: Capsid protein VP1
4: Capsid protein VP1
5: Capsid protein VP1
6: Capsid protein VP1
7: Minor capsid protein VP2
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)16,945,0231140
Polymers16,714,405420
Non-polymers230,617720
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
1: Capsid protein VP1
2: Capsid protein VP1
3: Capsid protein VP1
4: Capsid protein VP1
5: Capsid protein VP1
6: Capsid protein VP1
7: Minor capsid protein VP2
hetero molecules
x 5


  • icosahedral pentamer
  • 1.41 MDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)1,412,08595
Polymers1,392,86735
Non-polymers19,21860
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: Capsid protein VP1
2: Capsid protein VP1
3: Capsid protein VP1
4: Capsid protein VP1
5: Capsid protein VP1
6: Capsid protein VP1
7: Minor capsid protein VP2
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 1.69 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,694,502114
Polymers1,671,44142
Non-polymers23,06272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Capsid protein VP1


Mass: 40053.449 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) BK polyomavirus / Cell line: Vero / References: UniProt: Q65613, UniProt: P03088*PLUS
#2: Protein Minor capsid protein VP2 / Minor structural protein VP2


Mass: 38252.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BK polyomavirus / Cell line: Vero / References: UniProt: P03094
#3: Polysaccharide
N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid


Type: oligosaccharide / Mass: 600.525 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-8DNeup5Aca2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[Aad21122h-2a_2-6_5*NCC/3=O]/1-1/a8-b2WURCSPDB2Glycan 1.1.0
[][<C11N1O7>]{[(1+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: BK polyomavirus / Type: VIRUS / Entity ID: #1-#2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Human polyomavirus 1
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: Icosahedron / Diameter: 500 nm / Triangulation number (T number): 7
Buffer solutionpH: 7.5
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 59 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40334 / Symmetry type: POINT

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