9MQ8 | pdb_00009mq8

Cryo-EM structure of hemagglutinin H5N1 in complex with Fab 310-33-1_H02

• PDB DOI: https://doi.org/10.2210/pdb9MQ8/pdb
• EM Map EMD-48516: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Influenza A virus, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-01-02 Released: 2025-08-13 
• Deposition Author(s): Malla, T.N., Tsybovsky, Y., Zhou, T.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.73 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Cross-neutralizing and potent human monoclonal antibodies against historical and emerging H5Nx influenza viruses.

Abu-Shmais, A.A., Freeman, G., Creanga, A., Vukovich, M.J., Malla, T., Mantus, G.E., Shimberg, G.D., Gillespie, R.A., Guerra Canedo, V., Dadonaite, B., Rodgers, M.D., Chopde, A.J., Bardwil-Lugones, E., Bylund, T., Henry, A.R., Roberts-Torres, J., Johnston, T.S., Smith, S., Yang, E.S., Cheng, C., Walker, E.L., Ravichandran, M., Gordon, I.J., Dittakavi, T.S., Reed, D.S., Pierson, T.C., Dropulic, L., Bloom, J.D., Tsybovsky, Y., Boritz, E.A., Douek, D.C., Zhou, T., Kanekiyo, M., Andrews, S.F.

(2025) Nat Microbiol 10: 2903-2918

• PubMed: 41087744 
• DOI: https://doi.org/10.1038/s41564-025-02137-x
• Primary Citation Related Structures: 
  9MQ7, 9MQ8, 9MQ9, 9MQA, 9MQD


• PubMed Abstract: 
  

  Highly pathogenic avian influenza H5Nx viruses are an emerging threat for global health, especially clade 2.3.4.4b H5N1 virus which causes panzootic infections. Here we describe the isolation and characterization of broadly cross-neutralizing monoclonal antibodies (mAbs) against diverse H5Nx viruses from individuals who received a monovalent H5N1 vaccine 15 years ago. By screening over 500 mAbs, we identified 5 mAbs that neutralized the majority of H5 clades including 2.3.4.4b and target three distinct conserved epitopes within the HA globular head. Cryo-electron microscopy structures of these mAbs in complex with HA, deep mutational scanning and neutralization escape studies define the sites of vulnerability of H5 HA. These mAbs mediated stronger prophylactic protection against clade 2.3.4.4b H5N1 infection in mice than the best-in-class mAb targeting the HA stem. Our study identified several highly potent broadly neutralizing H5 mAbs from humans that either alone or in combination provide a pragmatic pandemic preparedness option against the threat of panzootic H5N1 influenza.

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Organizational Affiliation: 
• Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
Fred Hutchinson Cancer Center, Seattle, WA, USA.
Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA.
Howard Hughes Medical Institute, Chevy Chase, MD, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. [e-mail].
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. [e-mail].
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 12-mer - A6B3C3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 269.99 kDa 
• Atom Count: 14,479 
• Modeled Residue Count: 1,842 
• Deposited Residue Count: 2,412 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 chain	A, C, E	342	Influenza A virus	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A0A8E4ZAK5 (Influenza A virus) Explore A0A8E4ZAK5  Go to UniProtKB:  A0A8E4ZAK5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	B, D, F	227	Influenza A virus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
310-33-1_H02 Fab Heavy chain	G [auth H], H [auth I], I [auth J]	124	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
310-33-1_H02 Fab Light chain	J [auth L], K [auth M], L [auth N]	111	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.73 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Malla, T.N., Tsybovsky, Y., Zhou, T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release
  
• Version 1.1: 2026-08-26
  Changes: Data collection, Database references