9LHO | pdb_00009lho

CryoEM structure of H7 hemagglutinin in complex with a human neutralizing antibody 6Y13


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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

Structural basis for a potent human neutralizing antibody targeting a conserved epitope on the H7 hemagglutinin head.

Li, J.Wang, M.Yang, Y.Zhang, L.Liu, L.Yang, W.Peng, Y.Zhang, X.Yuan, B.Peng, Q.Yang, X.Chen, Y.Gao, G.F.Shi, Y.Wan, X.

(2025) Proc Natl Acad Sci U S A 122: e2503008122-e2503008122

  • DOI: https://doi.org/10.1073/pnas.2503008122
  • Primary Citation of Related Structures:  
    9LHO

  • PubMed Abstract: 

    Zoonotic H7N9 avian influenza virus infection remains a global concern because of its pandemic potential. Therefore, developing effective antibodies and vaccines against H7N9 is vital for preventing and controlling major outbreaks. Here, we isolated a human VH3-30 gene-encoded antibody, designated 6Y13, from a survivor of H7N9 infection. This antibody recognized the hemagglutinins (HAs) of the representative H7 subtype zoonotic viruses spanning two decades of antigenic evolution and potently neutralized epidemic H7N9 viruses in vitro. Moreover, 6Y13 conferred complete protection in mice against lethal H7N9 challenge in both prophylactic and therapeutic experiments. Structural analysis by cryoelectron microscopy indicated that 6Y13 binds to a unique conserved site on the HA head, distinct from the receptor-binding site and lateral patch. Nevertheless, 6Y13 efficiently blocked viral receptor binding without interfering with HA receptor binding, independent of Fc-mediated steric hindrance. Our findings provide a promising therapeutic candidate against pan-H7 subtype viruses and are beneficial for the design of H7 subtype influenza vaccine immunogens.


  • Organizational Affiliation
    • Shenzhen Key Laboratory of Human Antibody Engineering, Center for Protein and Cell-Based Drugs, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin505Influenza A virus (A/duck/Chiba/25-51-14/2013(H7N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for N0DP11 (Influenza A virus)
Explore N0DP11 
Go to UniProtKB:  N0DP11
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupN0DP11
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
scFv of 6Y13 chimera264Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
M [auth A]
N [auth A]
O [auth B]
P [auth C]
Q [auth C]
M [auth A],
N [auth A],
O [auth B],
P [auth C],
Q [auth C],
R [auth D],
S [auth E],
T [auth E],
U [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32192452

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release