6ESB

BK polyomavirus + 20 mM GT1b oligosaccharide

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

The Structure of an Infectious Human Polyomavirus and Its Interactions with Cellular Receptors.

Hurdiss, D.L., Frank, M., Snowden, J.S., Macdonald, A., Ranson, N.A.

(2018) Structure 26: 839-847.e3

  • DOI: 10.1016/j.str.2018.03.019
  • Primary Citation of Related Structures:  
    6ESB

  • PubMed 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 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 ...

    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.

    Organizational Affiliation: 

    Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. Electronic address: n.a.ranson@leeds.ac.uk.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid protein VP1361Human polyomavirus 1Mutation(s): 0 
UniProt
Find proteins for P03088 (BK polyomavirus)
Explore P03088 
Go to UniProtKB:  P03088
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03088
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Minor capsid protein VP2G [auth 7]350Human polyomavirus 1Mutation(s): 0 
UniProt
Find proteins for P03094 (BK polyomavirus)
Explore P03094 
Go to UniProtKB:  P03094
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03094
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid
H [auth A],
I [auth B],
J [auth C],
K [auth D],
L [auth E],
H [auth A],
I [auth B],
J [auth C],
K [auth D],
L [auth E],
M [auth F]
2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G87492XO
GlyCosmos:  G87492XO
GlyGen:  G87492XO
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom102572/B/13/Z

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-05-09
    Changes: Data collection, Database references
  • Version 1.2: 2018-06-13
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary