Experimental Data Snapshot

  • Resolution: 3.65 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.244 

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Crystal structures of murine polyomavirus in complex with straight-chain and branched-chain sialyloligosaccharide receptor fragments.

Stehle, T.Harrison, S.C.

(1996) Structure 4: 183-194

  • DOI: https://doi.org/10.1016/s0969-2126(96)00021-4
  • Primary Citation of Related Structures:  
    1SID, 1SIE

  • PubMed Abstract: 

    Murine polyomavirus recognizes (alpha2,3)-linked alpha-5-N-acetylneuraminic acid (sialic acid) on the surface of susceptible cells. While all strains bind to straight-chain receptors terminating in (alpha2,3)-linked sialic acid, some strains also bind to branched oligosaccharides that carry a second, (alpha2,6)-linked sialic acid. The ability to bind to these branched-chain receptors correlates with a single amino acid mutation at position 91 on the outer surface of the major capsid protein, VP1, and with a significant decrease in tumorigenicity. We have determined the structures of polyomavirus strain P16, which bears a glycine at position 91, in complex with model compounds for both straight-chain and branched-chain sialoglycoconjugates. The structures have been refined to a resolution of 3.65 degree. The ligands bind to a shallow groove on the surface of VP1. The sialic acid-(alpha2,3)-galactose moiety, which is common to both compounds, has specific and identical contacts. The additional (alpha2,6)-linked sialic acid moiety of the branched-chain receptor fragment fits into a surface pocket, but it has high thermal factors and does not form hydrogen bonds to groups on VP1. Data collected from crystals soaked at different oligosaccharide concentrations establish that both receptor fragments have similar, low affinities (dissociation constants in the range 5-10 mM) for the P16 virus, consistent with the interactions seen in the two complexes. The oligosaccharide-binding groove is complementary to the shape of the bound glycan, but there are relatively few hydrogen bonds between glycan and protein. Thus, the nature of the glycosidic linkages appears to be the principal determinant of specificity, rather than the position of particular hydroxyl groups. The low receptor affinity may be important for avoiding inhibition of viral release by retention on surface receptors of infected cells. Evidence suggests that strains with still greater pathogenicity are likely to have even weaker affinity.

  • Organizational Affiliation

    Howard Hughes Medical Institute and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
383Mouse polyomavirus (strain p16 small-plaque)Mutation(s): 0 
Find proteins for P49302 (Murine polyomavirus (strain P16 small-plaque))
Explore P49302 
Go to UniProtKB:  P49302
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49302
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, I, J, K
G, H, I, J, K, L
Glycosylation Resources
GlyTouCan:  G14000ZZ
GlyCosmos:  G14000ZZ
GlyGen:  G14000ZZ
Experimental Data & Validation

Experimental Data

  • Resolution: 3.65 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.244 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 570α = 90
b = 570β = 90
c = 570γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-06-20
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Structure summary