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

Potently Neutralizing Pan H5 monoclonal antibodies provide protection against HPAI H5N1

Abu-Shmais, A., Malla, T., Tsybovsky, Y., Zhou, T., Andrews, S., Kanekiyo, M.

To be published.

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