3NXD

JC polyomavirus VP1 in complex with LSTc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-function analysis of the human JC polyomavirus establishes the LSTc pentasaccharide as a functional receptor motif.

Neu, U.Maginnis, M.S.Palma, A.S.Stroh, L.J.Nelson, C.D.Feizi, T.Atwood, W.J.Stehle, T.

(2010) Cell Host Microbe 8: 309-319

  • DOI: 10.1016/j.chom.2010.09.004
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The human JC polyomavirus (JCV) causes a fatal demyelinating disease, progressive multifocal leukoencephalopathy (PML), in immunocompromised individuals. Current treatment options for PML are inadequate. Sialylated oligosaccharides and the serotonin ...

    The human JC polyomavirus (JCV) causes a fatal demyelinating disease, progressive multifocal leukoencephalopathy (PML), in immunocompromised individuals. Current treatment options for PML are inadequate. Sialylated oligosaccharides and the serotonin receptor are known to be necessary for JCV entry, but the molecular interactions underlying JCV attachment remain unknown. Using glycan array screening and viral infectivity assays, we identify a linear sialylated pentasaccharide with the sequence NeuNAc-α2,6-Gal-β1,4-GlcNAc-β1,3-Gal-β1,4-Glc (LSTc) present on host glycoproteins and glycolipids as a specific JCV recognition motif. The crystal structure of the JCV capsid protein VP1 was solved alone and in complex with LSTc. It reveals extensive interactions with the terminal sialic acid of the LSTc motif and specific recognition of an extended conformation of LSTc. Mutations in the JCV oligosaccharide-binding sites abolish cell attachment, viral spread, and infectivity, further validating the importance of this interaction. Our findings provide a powerful platform for the development of antiviral compounds.


    Organizational Affiliation

    Interfaculty Institute for Biochemistry, University of Tübingen, D-72076 Tübingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major capsid protein VP1
C, B, A, D, E
272JC polyomavirusMutation(s): 0 
Find proteins for P03089 (JC polyomavirus)
Go to UniProtKB:  P03089
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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A, B, C, D, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BGC
Query on BGC

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Download CCD File 
B, C
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
GAL
Query on GAL

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Download CCD File 
B, C
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, C, D, E
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
B, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SIA
Query on SIA

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Download CCD File 
B, C
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 149.670α = 90.00
b = 96.340β = 110.28
c = 128.220γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
RemDAqdata collection
XSCALEdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance