8YGT | pdb_00008ygt

Cryo-EM structure of simian rotavirus SA11 VP4 in complex with nAb 7H13-I54G mutant (left side)

• PDB DOI: https://doi.org/10.2210/pdb8YGT/pdb
• EM Map EMD-39263: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Rotavirus A, Mus musculus
• Expression System: Mus musculus
• Mutation(s): No 


• Deposited: 2024-02-27 Released: 2025-02-12 
• Deposition Author(s): Huang, Y., Sun, H., Zheng, Q., Li, S., Ge, S., Xia, N.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.01 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A single residue switch mediates the broad neutralization of Rotaviruses.

Huang, Y., Song, F., Zeng, Y., Sun, H., Sheng, R., Wang, X., Liu, L., Luo, G., Jiang, Y., Chen, Y., Zhang, M., Zhang, S., Gu, Y., Yu, H., Li, S., Li, T., Zheng, Q., Ge, S., Zhang, J., Xia, N.

(2025) Nat Commun 16: 838-838

• PubMed: 39833145 
• DOI: https://doi.org/10.1038/s41467-025-56114-3
• Primary Citation of Related Structures:  
  8YGR, 8YGS, 8YGT, 8YGU


• PubMed Abstract: 
  

  Broadly neutralizing antibodies (bNAbs) could offer escape-tolerant and lasting protection against viral infections and therefore guide development of broad-spectrum vaccines. The increasing challenge posed by viral evolution and immune evasion intensifies the importance of the discovery of bNAbs and their underlying neutralization mechanism. Here, focusing on the pivotal viral protein VP4 of rotavirus (RV), we identify a potent bNAb, 7H13, exhibiting broad-spectrum neutralization across diverse RV genotypes and demonstrating strong prevention of virus infection in female mice. A combination of time-resolved cryo-electron microscopy (cryo-EM) and in situ cryo-electron tomography (cryo-ET) analysis reveals a counterintuitive dynamic process of virus inactivation, in which 7H13 asymmetrically binds to a conserved epitope in the capsid-proximal aspect of VP4, triggers a conformational switch in a critical residue-F418-thereby disrupts the meta-stable conformation of VP4 essential for normal viral infection. Structure-guided mutagenesis corroborates the essential role of the 7H13 heavy chain I54 in activating F418 switch and destabilizing VP4. These findings define an atypical NAbs' neutralization mechanism and reveal a potential type of virus vulnerable site for universal vaccine and therapeutics design.

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Organizational Affiliation: 
• State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China.
National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China.
Collaborative Innovation Center for Translation Medical Testing and Application Technology, Department of Medical Technology, Zhangzhou Health Vocational College, Zhangzhou, PR China.
Novel Product R&D Department, Xiamen Innovax Biotech Co., Ltd., Xiamen, PR China.
State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China. [e-mail].
National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China. [e-mail].
State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China. [e-mail].
National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China. [e-mail].
State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China. [e-mail].
National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China. [e-mail].
State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China. [e-mail].
National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China. [e-mail].
State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China. [e-mail].
National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China. [e-mail].
State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China. [e-mail].
National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China. [e-mail].
Research Unit of Frontier Technology of Structural Vaccinology, Chinese Academy of Medical Sciences, Xiamen, Fujian, PR China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 154.19 kDa 
• Atom Count: 3,518 
• Modeled Residue Count: 449 
• Deposited Residue Count: 1,385 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer capsid protein VP4	A, B	581	Rotavirus A	Mutation(s): 0
UniProt
Find proteins for A2T3T2 (Rotavirus A (isolate RVA/Monkey/South Africa/SA11-H96/1958/G3P5B[2])) Explore A2T3T2  Go to UniProtKB:  A2T3T2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody 7H13-I54G mutant heavy chain	C [auth H]	116	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody 7H13-I54G mutant light chain	D [auth L]	107	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.01 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Huang, Y., Sun, H., Zheng, Q., Li, S., Ge, S., Xia, N.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release