9W4I | pdb_00009w4i

Cryo-EM structure of Enterovirus-D68 MO strain virus-like particle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

Comparative immunogenic and structural analysis of virus-like particle and inactivated whole-virion vaccines against enterovirus D68.

Senpuku, K.Kunishima, Y.Hirose, M.Karaki, T.Taniguchi, K.Kataoka-Nakamura, C.Hirai, T.Yasuda, K.Kuroda, E.Kato, T.Ito, T.Yoshioka, Y.

(2026) Mol Ther Nucleic Acids 37: 102957-102957

  • DOI: https://doi.org/10.1016/j.omtn.2026.102957
  • Primary Citation Related Structures: 
    9W4I

  • PubMed Abstract: 

    Enterovirus D68 (EV-D68) primarily causes respiratory illnesses and has been implicated in acute flaccid myelitis. Although virus-like particle (VLP) and traditional inactivated whole-virion (IWV) vaccines have demonstrated efficacy in mice, their immunological differences remain undetermined. Here, we directly compared the immunogenic and structural properties of VLP and IWV vaccines derived from the same EV-D68 strain under identical conditions. Although VLP induced significantly lower levels of EV-D68-specific IgG than IWV, neutralizing antibody titers and protective effects against viral challenge were comparable between the two groups in mice. Passive transfer experiments in neonatal mice further confirmed protection against lethal infection for both vaccine groups. Notably, in contrast to the IWV vaccine, the VLP vaccine elicited antibodies that preferentially recognized a limited subset of epitopes. Cryo-electron microscopy analyses revealed that VLPs structurally resemble the native virus but display distinct features in regions corresponding to epitopes that show differential antibody reactivity between VLP and IWV vaccines. By integrating structural and immunological analyses, we established a mechanistic framework linking capsid architecture to vaccine-induced antibody specificity. These findings suggest that VLP is a promising EV-D68 vaccine antigen with distinct epitope recognition profiles driven by structural characteristics.


  • Organizational Affiliation
    • Laboratory of Nano-design for Innovative Drug Development, Graduate School of Pharmaceutical Sciences, The University of Osaka, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.

Macromolecule Content 

  • Total Structure Weight: 95.05 kDa 
  • Atom Count: 4,856 
  • Modeled Residue Count: 620 
  • Deposited Residue Count: 861 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid protein VP1297enterovirus D68Mutation(s): 0 
UniProt
Find proteins for A0A097BW12 (Human enterovirus D68)
Explore A0A097BW12 
Go to UniProtKB:  A0A097BW12
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A097BW12
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid protein VP0317enterovirus D68Mutation(s): 0 
EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for A0A097BW12 (Human enterovirus D68)
Explore A0A097BW12 
Go to UniProtKB:  A0A097BW12
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A097BW12
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid protein VP3247enterovirus D68Mutation(s): 0 
UniProt
Find proteins for A0A097BW12 (Human enterovirus D68)
Explore A0A097BW12 
Go to UniProtKB:  A0A097BW12
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A097BW12
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTISOLDE1.6
RECONSTRUCTIONcryoSPARC4.4.1

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP24K22020
Japan Science and TechnologyJapanJPMJSP2138

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-01
    Type: Initial release