4MJ0

BK Polyomavirus VP1 pentamer in complex with GD3 oligosaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

A Structure-Guided Mutation in the Major Capsid Protein Retargets BK Polyomavirus.

Neu, U.Allen, S.A.Blaum, B.S.Liu, Y.Frank, M.Palma, A.S.Stroh, L.J.Feizi, T.Peters, T.Atwood, W.J.Stehle, T.

(2013) PLoS Pathog 9: e1003688-e1003688

  • DOI: 10.1371/journal.ppat.1003688
  • Primary Citation of Related Structures:  
    4MJ0, 4MJ1

  • PubMed Abstract: 
  • Viruses within a family often vary in their cellular tropism and pathogenicity. In many cases, these variations are due to viruses switching their specificity from one cell surface receptor to another. The structural requirements that underlie such receptor switching are not well understood especially for carbohydrate-binding viruses, as methods capable of structure-specificity studies are only relatively recently being developed for carbohydrates ...

    Viruses within a family often vary in their cellular tropism and pathogenicity. In many cases, these variations are due to viruses switching their specificity from one cell surface receptor to another. The structural requirements that underlie such receptor switching are not well understood especially for carbohydrate-binding viruses, as methods capable of structure-specificity studies are only relatively recently being developed for carbohydrates. We have characterized the receptor specificity, structure and infectivity of the human polyomavirus BKPyV, the causative agent of polyomavirus-associated nephropathy, and uncover a molecular switch for binding different carbohydrate receptors. We show that the b-series gangliosides GD3, GD2, GD1b and GT1b all can serve as receptors for BKPyV. The crystal structure of the BKPyV capsid protein VP1 in complex with GD3 reveals contacts with two sialic acid moieties in the receptor, providing a basis for the observed specificity. Comparison with the structure of simian virus 40 (SV40) VP1 bound to ganglioside GM1 identifies the amino acid at position 68 as a determinant of specificity. Mutation of this residue from lysine in BKPyV to serine in SV40 switches the receptor specificity of BKPyV from GD3 to GM1 both in vitro and in cell culture. Our findings highlight the plasticity of viral receptor binding sites and form a template to retarget viruses to different receptors and cell types.


    Organizational Affiliation

    Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VP1 capsid proteinA, B, C, D, E275Human polyomavirus 1Mutation(s): 0 
Find proteins for P03088 (BK polyomavirus)
Explore P03088 
Go to UniProtKB:  P03088
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranoseF4 N/A Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acidG, I2 N/A Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranoseH3 N/A Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.68α = 90
b = 152.64β = 90
c = 63.19γ = 90
Software Package:
Software NamePurpose
RemDAqdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary