9M7V | pdb_00009m7v

Cryo-EM structure of enterovirus A71 mature virion in complex with Fab CT11F9


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 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

Development of In Vitro Potency Methods to Replace In Vivo Tests for Enterovirus 71 Inactivated Vaccine (Human Diploid Cell-Based/Vero Cell-Based).

Zhang, X.Yi, L.Yu, D.Li, J.Li, X.Wu, X.Gao, F.He, Q.Wang, W.Wang, K.Wang, Z.Liu, Z.Li, Y.Zhao, Y.Li, H.Ma, X.Zheng, Q.Xu, L.Cheng, T.Zhu, R.Guo, J.Li, J.Mao, Q.Liang, Z.

(2025) Vaccines (Basel) 13

  • DOI: https://doi.org/10.3390/vaccines13040404
  • Primary Citation of Related Structures:  
    9M7V

  • PubMed Abstract: 

    The three commercial Enterovirus 71 (EV71) inactivated vaccines which have effectively controlled the EV71 pandemic currently rely on inherent variable in vivo potency methods for batch release. To align with 3R (Replacement, Reduction, Refinement) principles and enhance quality control, this study referred to WHO guidelines and the European Pharmacopoeia to develop in vitro relative potency (IVRP) methods. Working standards tracing to phase 3 clinical vaccines were established. Manufacture-specific IVRP methods were developed and validated per ICH Q14/Q2(R2), utilizing conformational epitope-targeting neutralizing monoclonal antibodies (MAbs). One of the MAbs (CT11F9) recognition sites was clarified with Cryo-EM. Subsequently, the performance of IVRP was assessed using varied concentrations and heat-treated vaccines. The correlation between IVRP and in vivo methods was analyzed, followed by setting IVRP specifications. The manufacturer-specific working standard exhibited ED50 values comparable to those of related phase 3 clinical vaccines. All IVRP methods achieved a relative bias/precision/total error ≤ 15%. The IVRP methods correlated with in vivo methods ( p < 0.05, r > 0.9) can discriminate EV71 antigen concentrations ( p < 0.01, r > 0.99) and indicate the stability of the vaccines. Cryo-EM was adopted to identify the epitopes recognized by CT11F9, revealing that this neutralizing antibody recognizes a conformational epitope spanning VP1-3 of the same protomer. Using 31-47 batches of commercial vaccines, IVRP specifications were proposed as 0.56-1.35, 0.58-1.40, and 0.54-1.50. Based on conformational epitope-targeting neutralizing MAbs, manufacturer-specific IVRP methods, which were sensitive to process variations and correlated with in vivo results, have been established. IVRP methods provide a reliable, animal-free alternative for EV71 vaccine batch release.


  • Organizational Affiliation
    • NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, State Key Laboratory of Drug Regulatory Science, Research Units of Innovative Vaccine Quality Evaluation and Standardization, Chinese Academy of Medical Sciences, National Institutes for Food and Drug Control, Beijing 102629, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
The light chain of Fab CT11F9A [auth L]106Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
The heavy chain of Fab CT11F9B [auth H]119Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP1C [auth A]297Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for B9VUU3 (Human enterovirus 71)
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Go to UniProtKB:  B9VUU3
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UniProt GroupB9VUU3
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP2D [auth B]254Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for B9VUU3 (Human enterovirus 71)
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UniProt GroupB9VUU3
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP3E [auth C]242Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for B9VUU3 (Human enterovirus 71)
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UniProt GroupB9VUU3
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP4F [auth D]69Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for B9VUU3 (Human enterovirus 71)
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UniProt GroupB9VUU3
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-16
    Changes: Data collection