6ESB

BK polyomavirus + 20 mM GT1b oligosaccharide


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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 vac ...

    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

    Biognos AB, P.O. Box 8963, Gothenburg 40274, Sweden.,Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. Electronic address: a.macdonald@leeds.ac.uk.,Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP1
1, 2, 3, 4, 5, 6
361BK polyomavirusMutation(s): 0 
Find proteins for P03088 (BK polyomavirus)
Go to UniProtKB:  P03088
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Minor capsid protein VP2
7
350BK polyomavirusMutation(s): 0 
Find proteins for P03094 (BK polyomavirus)
Go to UniProtKB:  P03094
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
1, 2, 3, 4
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
SIA
Query on SIA

Download SDF File 
Download CCD File 
1, 2, 3, 4, 5, 6
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-05-09
    Type: Data collection, Database references
  • Version 1.2: 2018-06-13
    Type: Data collection, Database references