6CV3

CryoEM structure of human enterovirus D68 emptied particle

  • Classification: VIRUS
  • Organism(s): Enterovirus D68

  • Deposited: 2018-03-27 Released: 2019-07-24 
  • Deposition Author(s): Liu, Y., Rossmann, M.G.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases 

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.56 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Bypassing pan-enterovirus host factor PLA2G16.

Baggen, J.Liu, Y.Lyoo, H.van Vliet, A.L.W.Wahedi, M.de Bruin, J.W.Roberts, R.W.Overduin, P.Meijer, A.Rossmann, M.G.Thibaut, H.J.van Kuppeveld, F.J.M.

(2019) Nat Commun 10: 3171-3171

  • DOI: 10.1038/s41467-019-11256-z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Enteroviruses are a major cause of human disease. Adipose-specific phospholipase A2 (PLA2G16) was recently identified as a pan-enterovirus host factor and potential drug target. In this study, we identify a possible mechanism of PLA2G16 evasion by em ...

    Enteroviruses are a major cause of human disease. Adipose-specific phospholipase A2 (PLA2G16) was recently identified as a pan-enterovirus host factor and potential drug target. In this study, we identify a possible mechanism of PLA2G16 evasion by employing a dual glycan receptor-binding enterovirus D68 (EV-D68) strain. We previously showed that this strain does not strictly require the canonical EV-D68 receptor sialic acid. Here, we employ a haploid screen to identify sulfated glycosaminoglycans (sGAGs) as its second glycan receptor. Remarkably, engagement of sGAGs enables this virus to bypass PLA2G16. Using cryo-EM analysis, we reveal that, in contrast to sialic acid, sGAGs stimulate genome release from virions via structural changes that enlarge the putative openings for genome egress. Together, we describe an enterovirus that can bypass PLA2G16 and identify additional virion destabilization as a potential mechanism to circumvent PLA2G16.


    Organizational Affiliation

    Virology Division, Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands.,Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL, Utrecht, The Netherlands.,Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL, Utrecht, The Netherlands. f.j.m.vankuppeveld@uu.nl.,Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
viral protein 1
A
297Enterovirus D68Mutation(s): 0 
Find proteins for A0A0X7Z9B1 (Enterovirus D68)
Go to UniProtKB:  A0A0X7Z9B1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
viral protein 3
B
247Enterovirus D68Mutation(s): 0 
Find proteins for E9RIT6 (Enterovirus D68)
Go to UniProtKB:  E9RIT6
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
viral protein 2
C
248Enterovirus D68Mutation(s): 0 
Find proteins for A0A0X7Z9B1 (Enterovirus D68)
Go to UniProtKB:  A0A0X7Z9B1
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.56 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
PDB_EXTRACTdata extraction

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: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-07-31
    Type: Data collection, Database references