1VPS

POLYOMAVIRUS VP1 PENTAMER COMPLEXED WITH A DISIALYLATED HEXASACCHARIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

High-resolution structure of a polyomavirus VP1-oligosaccharide complex: implications for assembly and receptor binding.

Stehle, T.Harrison, S.C.

(1997) EMBO J 16: 5139-5148

  • DOI: 10.1093/emboj/16.16.5139
  • Primary Citation of Related Structures:  
    1VPS, 1VPN

  • PubMed Abstract: 
  • The crystal structure of a recombinant polyomavirus VP1 pentamer (residues 32-320) in complex with a branched disialylated hexasaccharide receptor fragment has been determined at 1.9 A resolution. The result extends our understanding of oligosaccharide receptor recognition ...

    The crystal structure of a recombinant polyomavirus VP1 pentamer (residues 32-320) in complex with a branched disialylated hexasaccharide receptor fragment has been determined at 1.9 A resolution. The result extends our understanding of oligosaccharide receptor recognition. It also suggests a mechanism for enhancing the fidelity of virus assembly. We have previously described the structure of the complete polyomavirus particle complexed with this receptor fragment at 3.65 A. The model presented here offers a much more refined view of the interactions that determine carbohydrate recognition and allows us to assign additional specific contacts, in particular those involving the (alpha2,6)-linked, branching sialic acid. The structure of the unliganded VP1 pentamer, determined independently, shows that the oligosaccharide fits into a preformed groove and induces no measurable structural rearrangements. A comparison with assembled VP1 in the virus capsid reveals a rearrangement of residues 32-45 at the base of the pentamer. This segment may help prevent the formation of incorrectly assembled particles by reducing the likelihood that the C-terminal arm will fold back into its pentamer of origin.


    Related Citations: 
    • The Structure of Simian Virus 40 Refined at 3.1 A Resolution
      Stehle, T., Gamblin, S.J., Yan, Y., Harrison, S.C.
      (1996) Structure 4: 165
    • 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
    • Structure of Murine Polyomavirus Complexed with an Oligosaccharide Receptor Fragment
      Stehle, T., Yan, Y., Benjamin, T.L., Harrison, S.C.
      (1994) Nature 369: 160

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
POLYOMAVIRUS VP1 PENTAMERA, B, C, D, E289Mus musculus polyomavirus 1Mutation(s): 0 
UniProt
Find proteins for P49302 (Murine polyomavirus (strain P16 small-plaque))
Explore P49302 
Go to UniProtKB:  P49302
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseF, G, H, I, J4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G14000ZZ
GlyCosmos:  G14000ZZ
GlyGen:  G14000ZZ
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 221.5α = 90
b = 221.5β = 90
c = 99.8γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-05-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    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, Derived calculations, Other, Structure summary