4X13

JC Polyomavirus genotype 3 VP1 in complex with LSTc pentasaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

The Greater Affinity of JC Polyomavirus Capsid for alpha 2,6-Linked Lactoseries Tetrasaccharide c than for Other Sialylated Glycans Is a Major Determinant of Infectivity.

Stroh, L.J.Maginnis, M.S.Blaum, B.S.Nelson, C.D.Neu, U.Gee, G.V.O'Hara, B.A.Motamedi, N.DiMaio, D.Atwood, W.J.Stehle, T.

(2015) J.Virol. 89: 6364-6375

  • DOI: 10.1128/JVI.00489-15
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The human JC polyomavirus (JCPyV) establishes an asymptomatic, persistent infection in the kidneys of the majority of the population and is the causative agent of the fatal demyelinating disease progressive multifocal leukoencephalopathy (PML) in imm ...

    The human JC polyomavirus (JCPyV) establishes an asymptomatic, persistent infection in the kidneys of the majority of the population and is the causative agent of the fatal demyelinating disease progressive multifocal leukoencephalopathy (PML) in immunosuppressed individuals. The Mad-1 strain of JCPyV, a brain isolate, was shown earlier to require α2,6-linked sialic acid on the lactoseries tetrasaccharide c (LSTc) glycan for attachment to host cells. In contrast, a JCPyV kidney isolate type 3 strain, WT3, has been reported to interact with sialic acid-containing gangliosides, but the role of these glycans in JCPyV infection has remained unclear. To help rationalize these findings and probe the effects of strain-specific differences on receptor binding, we performed a comprehensive analysis of the glycan receptor specificities of these two representative JCPyV strains using high-resolution X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, and correlated these data with the results of infectivity assays. We show here that capsid proteins of Mad-1 and WT3 JCPyV can both engage LSTc as well as multiple sialylated gangliosides. However, the binding affinities exhibit subtle differences, with the highest affinity observed for LSTc. Engagement of LSTc is a prerequisite for functional receptor engagement, while the more weakly binding gangliosides are not required for productive infection. Our findings highlight the complexity of virus-carbohydrate interactions and demonstrate that subtle differences in binding affinities, rather than the binding event alone, help determine tissue tropism and viral pathogenesis.


    Organizational Affiliation

    Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA.,Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA walter_atwood@brown.edu thilo.stehle@uni-tuebingen.de.,Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.,Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA walter_atwood@brown.edu thilo.stehle@uni-tuebingen.de.,Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major capsid protein
A, B, C, D, E
272JC polyomavirusMutation(s): 0 
Gene Names: VP1
Find proteins for P90498 (JC polyomavirus)
Go to UniProtKB:  P90498
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, D, E
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
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

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

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Download CCD File 
A, B, 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, E
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, E
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: 0.178 
  • R-Value Work: 0.157 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 150.120α = 90.00
b = 96.280β = 109.81
c = 128.140γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2015-05-27
    Type: Database references
  • Version 2.0: 2018-01-31
    Type: Atomic model, Author supporting evidence, Derived calculations