JC polyomavirus VP1 from a genotype 3 strain

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report

This is version 2.0 of the entry. See complete history


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: https://doi.org/10.1128/JVI.00489-15
  • Primary Citation of Related Structures:  
    4X0Y, 4X0Z, 4X10, 4X11, 4X12, 4X13, 4X14, 4X15, 4X16, 4X17

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid protein
A, B, C, D, E
272JC polyomavirus type 3Mutation(s): 0 
Gene Names: VP1
Find proteins for P90498 (JC polyomavirus)
Explore P90498 
Go to UniProtKB:  P90498
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP90498
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
GA [auth E],
N [auth B],
T [auth C],
Z [auth D]
C3 H8 O3
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
DA [auth E]
EA [auth E]
FA [auth E]
AA [auth D],
BA [auth D],
DA [auth E],
EA [auth E],
FA [auth E],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
O [auth B],
P [auth B],
R [auth C],
S [auth C],
U [auth C],
W [auth D],
X [auth D],
Y [auth D]
C2 H6 O2
Query on K

Download Ideal Coordinates CCD File 
CA [auth D],
HA [auth E],
K [auth A],
Q [auth B],
V [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.48α = 90
b = 96.83β = 110.55
c = 128.22γ = 90
Software Package:
Software NamePurpose
Cootmodel building
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History  (Full details and data files)

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