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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 / homologyPolyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid / Polyomavirus coat protein / Polyomavirus coat protein VP2 / Capsid protein VP1,Polyomavirus / caveolin-mediated endocytosis of virus by host cell / permeabilization of host organelle membrane involved in viral entry into host cell / viral entry via permeabilization of inner membrane / T=7 icosahedral viral capsid ...Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid / Polyomavirus coat protein / Polyomavirus coat protein VP2 / Capsid protein VP1,Polyomavirus / caveolin-mediated endocytosis of virus by host cell / permeabilization of host organelle membrane involved in viral entry into host cell / viral entry via permeabilization of inner membrane / T=7 icosahedral viral capsid / host cell endoplasmic reticulum membrane / pore formation by virus in membrane of host cell / integral to membrane of host cell / viral penetration into host nucleus / viral capsid / ion channel activity / protein complex oligomerization / host cell nucleus / virion attachment to host cell / structural molecule activity / DNA binding / integral component of membrane / Major capsid protein VP1 / Minor capsid protein VP2 / Capsid protein VP1
Function and homology information
Specimen sourceBK polyomavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.4 Å resolution
AuthorsHurdiss, D.L. / Ranson, N.A.
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 20, 2017 / Release: May 2, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 2, 2018Structure modelrepositoryInitial release
1.1May 9, 2018Structure modelData collection / Database referencescitation_citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
1.2Jun 13, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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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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Movie viewer
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)282,52525
Polyers278,5737
Non-polymers3,95218
Water0
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)16,951,5081500
Polyers16,714,405420
Non-polymers237,1021080
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
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)1,412,626125
Polyers1,392,86735
Non-polymers19,75990
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
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
  • 1.7 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,695,151150
Polyers1,671,44142
Non-polymers23,710108
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

#1: Protein/peptide
Capsid protein VP1 /


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


Mass: 38252.730 Da / Num. of mol.: 1 / Source: (natural) BK polyomavirus / Cell line: Vero / References: UniProt: P03094
#3: Chemical
ChemComp-SIA / O-SIALIC ACID


Mass: 309.270 Da / Num. of mol.: 12 / Formula: C11H19NO9
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Formula: Ca / Calcium

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: BK polyomavirusBK virus / Type: VIRUS / Entity ID: 1,2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Human polyomavirus 1
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: STRAIN / Virus 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
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
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
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 40334 / Symmetry type: POINT

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