RCSB PDB - 8YGS: Cryo-EM structure of simian rotavirus SA11 VP4 in complex with nAb 7H13

 8YGS

Cryo-EM structure of simian rotavirus SA11 VP4 in complex with nAb 7H13


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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

  • 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.


  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer capsid protein VP4
A, B
581Rotavirus AMutation(s): 0 
UniProt
Find proteins for A0A5J6BC68 (Rotavirus A)
Explore A0A5J6BC68 
Go to UniProtKB:  A0A5J6BC68
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5J6BC68
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Outer capsid protein VP4581Rotavirus AMutation(s): 0 
UniProt
Find proteins for A0A5J6BC68 (Rotavirus A)
Explore A0A5J6BC68 
Go to UniProtKB:  A0A5J6BC68
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5J6BC68
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody 7H13 heavy chainD [auth H],
F [auth M]
116Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody 7H13 light chainE [auth L],
G [auth N]
107Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

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