5BNO

Crystal structure of human enterovirus D68 in complex with 6'SLN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.254 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Sialic acid-dependent cell entry of human enterovirus D68.

Liu, Y.Sheng, J.Baggen, J.Meng, G.Xiao, C.Thibaut, H.J.van Kuppeveld, F.J.Rossmann, M.G.

(2015) Nat Commun 6: 8865-8865

  • DOI: 10.1038/ncomms9865
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human enterovirus D68 (EV-D68) is a causative agent of childhood respiratory diseases and has now emerged as a global public health threat. Nevertheless, knowledge of the tissue tropism and pathogenesis of EV-D68 has been hindered by a lack of studie ...

    Human enterovirus D68 (EV-D68) is a causative agent of childhood respiratory diseases and has now emerged as a global public health threat. Nevertheless, knowledge of the tissue tropism and pathogenesis of EV-D68 has been hindered by a lack of studies on the receptor-mediated EV-D68 entry into host cells. Here we demonstrate that cell surface sialic acid is essential for EV-D68 to bind to and infect susceptible cells. Crystal structures of EV-D68 in complex with sialylated glycan receptor analogues show that they bind into the 'canyon' on the virus surface. The sialic acid receptor induces a cascade of conformational changes in the virus to eject a fatty-acid-like molecule that regulates the stability of the virus. Thus, virus binding to a sialic acid receptor and to immunoglobulin-like receptors used by most other enteroviruses share a conserved mechanism for priming viral uncoating and facilitating cell entry.


    Organizational Affiliation

    Department of Chemistry, University of Texas at El Paso, 500 W. University Avenue, El Paso, Texas 79968-0519, USA.,Department of Biological Sciences, Hockmeyer Hall of Structural Biology, 240 South Martin Jischke Drive, Purdue University, West Lafayette, Indiana 47907, USA.,Department of Infectious Diseases and Immunology, Virology Division, Faculty of Veterinary Medicine, Utrecht University, 3584CL Utrecht, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP1
A
297Enterovirus D68Mutation(s): 0 
Find proteins for Q68T42 (Enterovirus D68)
Go to UniProtKB:  Q68T42
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP2
B
248Enterovirus D68Mutation(s): 0 
Find proteins for Q68T42 (Enterovirus D68)
Go to UniProtKB:  Q68T42
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP3
C
247Enterovirus D68Mutation(s): 0 
Find proteins for Q68T42 (Enterovirus D68)
Go to UniProtKB:  Q68T42
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP4
D
68Enterovirus D68Mutation(s): 0 
Find proteins for Q68T42 (Enterovirus D68)
Go to UniProtKB:  Q68T42
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4U1
Query on 4U1

Download SDF File 
Download CCD File 
C
(6R)-5-(acetylamino)-3,5-dideoxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]-beta-L-threo-hex-2-ulopyranonosyl-(2->6)-beta-D-galactopyranosyl-(1->4)-2-(acetylamino)-2-deoxy-beta-D-glucopyranose
C25 H42 N2 O19
RPSBVJXBTXEJJG-LURNZOHQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.254 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 325.700α = 90.00
b = 347.400β = 90.00
c = 356.500γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
PDB_EXTRACTdata extraction
CNSphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI011219

Revision History 

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2015-11-25
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Other