Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D5  (3D View)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 151.15 kDa 
• Atom Count: 11187 
• Modelled Residue Count: 1291 
• Deposited Residue Count: 1360 
• Unique protein chains: 1

3NXG

JC polyomavirus VP1

• DOI: 10.2210/pdb3NXG/pdb

• Classification: VIRAL PROTEIN
• Organism(s): JC polyomavirus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-07-13 Released: 2010-11-17 
• Deposition Author(s): Neu, U., Stroeh, L.J., Stehle, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.207 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 

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

• PubMed: 20951965 
• DOI: 10.1016/j.chom.2010.09.004
• Primary Citation of Related Structures:  
  3NXG, 3NXD


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein VP1	A, B, C, D, E	272	JC polyomavirus	Mutation(s): 0  Gene Names: VP1
Find proteins for P03089 (JC polyomavirus) Explore P03089  Go to UniProtKB:  P03089

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A, B, C, D, E	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	A, C, D, E	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.207 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.57	α = 90
b = 96.02	β = 110.44
c = 128.55	γ = 90

Software Package:

Software Name	Purpose
RemDAq	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-07-13 
• Released Date: 2010-11-17 
Deposition Author(s): Neu, U., Stroeh, L.J., Stehle, T.

Revision History  

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