9C8F | pdb_00009c8f

Cryo-EM Structure of EV-D68 B3 A-Particle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 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

Structural insights from vaccine candidates for EV-D68.

Cheng, J.Krug, P.W.Lei, H.Moss, D.L.Lang, Z.C.Morton, A.J.Shen, C.H.Pletnev, S.Huang, R.K.Pierson, T.C.Zhou, T.Ruckwardt, T.J.Kwong, P.D.

(2025) Commun Biol 8: 860-860

  • DOI: https://doi.org/10.1038/s42003-025-08253-y
  • Primary Citation of Related Structures:  
    9C3J, 9C4A, 9C8F, 9C8G, 9C8H, 9C8I

  • PubMed Abstract: 

    Enterovirus D68 (EV-D68), a member of the Picornaviridae family, causes respiratory illness and can lead to acute flaccid myelitis in children. No specific treatment or vaccine is available. Here, we determine cryo-EM structures of EV-D68 virus-like particles (VLPs), inactivated virus particles (InVPs), and altered virus particles (A-particles) from B3 and A2 subclades. The B3 VLP is a current vaccine candidate, which we show closely resembles its InVP counterpart, particularly at the 5-fold axis of symmetry, the target of potent neutralizing antibodies. Similar structural conservation was observed in the A2 subclade. Sequence variation between B3 and A2 mainly occurred in flexible loops displayed on the particle surface. A canyon-filling pocket factor was present in B3 InVP but absent in A2 InVP. A-particles were predominant in β-propiolactone-inactivated virus at longer but not shorter incubation. Overall, our findings highlight EV-D68 similarities and subclade-specific differences, offering structural insights that relate to vaccine development.


  • Organizational Affiliation
    • Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VP1295enterovirus D68Mutation(s): 0 
UniProt
Find proteins for A0A4D5YIF3 (Human enterovirus D68)
Explore A0A4D5YIF3 
Go to UniProtKB:  A0A4D5YIF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4D5YIF3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VP2248enterovirus D68Mutation(s): 0 
UniProt
Find proteins for A0A890CN88 (Human enterovirus D68)
Explore A0A890CN88 
Go to UniProtKB:  A0A890CN88
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A890CN88
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VP3247enterovirus D68Mutation(s): 0 
UniProt
Find proteins for A0A5C0Q0H5 (Human enterovirus D68)
Explore A0A5C0Q0H5 
Go to UniProtKB:  A0A5C0Q0H5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5C0Q0H5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-12-03
    Changes: Data collection, Database references