7YHK | pdb_00007yhk

Cryo-EM structure of the HA trimer of A/Beijing/262/1995(H1N1) in complex with neutralizing antibody 12H5


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7YHK

This is version 1.2 of the entry. See complete history

Literature

Identification of a cross-neutralizing antibody that targets the receptor binding site of H1N1 and H5N1 influenza viruses.

Li, T.Chen, J.Zheng, Q.Xue, W.Zhang, L.Rong, R.Zhang, S.Wang, Q.Hong, M.Zhang, Y.Cui, L.He, M.Lu, Z.Zhang, Z.Chi, X.Li, J.Huang, Y.Wang, H.Tang, J.Ying, D.Zhou, L.Wang, Y.Yu, H.Zhang, J.Gu, Y.Chen, Y.Li, S.Xia, N.

(2022) Nat Commun 13: 5182-5182

  • DOI: https://doi.org/10.1038/s41467-022-32926-5
  • Primary Citation Related Structures: 
    7FAH, 7YHK

  • PubMed Abstract: 

    Influenza A viruses pose a significant threat globally each year, underscoring the need for a vaccine- or antiviral-based broad-protection strategy. Here, we describe a chimeric monoclonal antibody, C12H5, that offers neutralization against seasonal and pandemic H1N1 viruses, and cross-protection against some H5N1 viruses. Notably, C12H5 mAb offers broad neutralizing activity against H1N1 and H5N1 viruses by controlling virus entry and egress, and offers protection against H1N1 and H5N1 viral challenge in vivo. Through structural analyses, we show that C12H5 engages hemagglutinin (HA), the major surface glycoprotein on influenza, at a distinct epitope overlapping the receptor binding site and covering the 140-loop. We identified eight highly conserved (~90%) residues that are essential for broad H1N1 recognition, with evidence of tolerance for Asp or Glu at position 190; this site is a molecular determinant for human or avian host-specific recognition and this tolerance endows C12H5 with cross-neutralization potential. Our results could benefit the development of antiviral drugs and the design of broad-protection influenza vaccines.


  • Organizational Affiliation
    • State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, School of Public Health, Xiamen University, 361102, Xiamen, Fujian, China.

Macromolecule Content 

  • Total Structure Weight: 88.64 kDa 
  • Atom Count: 4,834 
  • Modeled Residue Count: 604 
  • Deposited Residue Count: 785 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
12H5 light chainA [auth F]117Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
12H5 heavy chainB [auth H]113Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
HemagglutininC [auth A]555Influenza A virus (A/Beijing/262/1995(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for Q6WG01 (Influenza A virus)
Explore Q6WG01 
Go to UniProtKB:  Q6WG01
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6WG01
Glycosylation
Glycosylation Sites: 5
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth B]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 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: 2022-08-17
    Type: Initial release
  • Version 1.1: 2023-07-19
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary