4X13

JC Polyomavirus genotype 3 VP1 in complex with LSTc pentasaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 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 3.0 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:  
    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 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

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major capsid proteinA, B, C, D, E272JC polyomavirus type 3Mutation(s): 0 
Gene Names: VP1
UniProt
Find proteins for P90498 (JC polyomavirus)
Explore P90498 
Go to UniProtKB:  P90498
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranoseF, G5N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G83513YI
GlyCosmos:  G83513YI
GlyGen:  G83513YI
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranoseH4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G03509EL
GlyCosmos:  G03509EL
GlyGen:  G03509EL
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth C] , CA [auth D] , DA [auth D] , FA [auth D] , HA [auth E] , I [auth A] , M [auth A] , T [auth B] , 
AA [auth C], CA [auth D], DA [auth D], FA [auth D], HA [auth E], I [auth A], M [auth A], T [auth B], U [auth B], X [auth C], Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
EA [auth D] , IA [auth E] , J [auth A] , JA [auth E] , K [auth A] , KA [auth E] , L [auth A] , LA [auth E] , 
EA [auth D], IA [auth E], J [auth A], JA [auth E], K [auth A], KA [auth E], L [auth A], LA [auth E], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], V [auth B], Y [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
BA [auth C], GA [auth D], MA [auth E], N [auth A], W [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 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 = 150.12α = 90
b = 96.28β = 109.81
c = 128.14γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
PHASERphasing
XDSdata reduction

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
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary