6CRP

CryoEM structure of human enterovirus D68 abortive product 1 (pH 7.2 and 4 degrees Celsius)

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

  • Deposited: 2018-03-19 Released: 2018-12-19 
  • Deposition Author(s): Liu, Y., Rossmann, M.G.
  • Funding Organization(s): National Institutes of Health/National Human Genome Research Institute 

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular basis for the acid-initiated uncoating of human enterovirus D68.

Liu, Y.Sheng, J.van Vliet, A.L.W.Buda, G.van Kuppeveld, F.J.M.Rossmann, M.G.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: E12209-E12217

  • DOI: 10.1073/pnas.1803347115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Enterovirus D68 (EV-D68) belongs to a group of enteroviruses that contain a single positive-sense RNA genome surrounded by an icosahedral capsid. Like common cold viruses, EV-D68 mainly causes respiratory infections and is acid-labile. The molecular ...

    Enterovirus D68 (EV-D68) belongs to a group of enteroviruses that contain a single positive-sense RNA genome surrounded by an icosahedral capsid. Like common cold viruses, EV-D68 mainly causes respiratory infections and is acid-labile. The molecular mechanism by which the acid-sensitive EV-D68 virions uncoat and deliver their genome into a host cell is unknown. Using cryoelectron microscopy (cryo-EM), we have determined the structures of the full native virion and an uncoating intermediate [the A (altered) particle] of EV-D68 at 2.2- and 2.7-Å resolution, respectively. These structures showed that acid treatment of EV-D68 leads to particle expansion, externalization of the viral protein VP1 N termini from the capsid interior, and formation of pores around the icosahedral twofold axes through which the viral RNA can exit. Moreover, because of the low stability of EV-D68, cryo-EM analyses of a mixed population of particles at neutral pH and following acid treatment demonstrated the involvement of multiple structural intermediates during virus uncoating. Among these, a previously undescribed state, the expanded 1 ("E1") particle, shows a majority of internal regions (e.g., the VP1 N termini) to be ordered as in the full native virion. Thus, the E1 particle acts as an intermediate in the transition from full native virions to A particles. Together, the present work delineates the pathway of EV-D68 uncoating and provides the molecular basis for the acid lability of EV-D68 and of the related common cold viruses.


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907; mr@purdue.edu.,Department of Biological Sciences, Purdue University, West Lafayette, IN 47907.,Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
viral protein 1
A
297Enterovirus D68Mutation(s): 0 
Find proteins for A0A097BW12 (Enterovirus D68)
Go to UniProtKB:  A0A097BW12
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
viral protein 3
B
247Enterovirus D68Mutation(s): 0 
Find proteins for A0A097BW12 (Enterovirus D68)
Go to UniProtKB:  A0A097BW12
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
viral protein 2
C
248Enterovirus D68Mutation(s): 0 
Find proteins for A0A097BW12 (Enterovirus D68)
Go to UniProtKB:  A0A097BW12
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
viral protein 4
D
68Enterovirus D68Mutation(s): 0 
Find proteins for A0A097BW12 (Enterovirus D68)
Go to UniProtKB:  A0A097BW12
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
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 Human Genome Research InstituteUnited StatesAI011219

Revision History 

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2018-12-26
    Type: Data collection, Database references
  • Version 1.2: 2019-01-09
    Type: Data collection, Database references