12IE | pdb_000012ie

Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-4C2 Fab fragments

• PDB DOI: https://doi.org/10.2210/pdb12IE/pdb
• EM Map EMD-76454: EMDB EMDataResource

• Classification: Immune System/Viral Protein
• Organism(s): Mus musculus, Influenza B virus (B/Lee/1940)
• Expression System: Mus musculus, Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2026-04-07 Released: 2026-08-26 
• Deposition Author(s): Civljak, A., Bonnettaz, B., Bajic, G.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.61 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-4C2 Fab fragments

Civljak, A., Bonnettaz, B., Bajic, G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 9-mer - A6B3 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 249.59 kDa 
• Atom Count: 14,643 
• Modeled Residue Count: 1,878 
• Deposited Residue Count: 2,259 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KL-BHA-4C2 heavy chain	A [auth H], H [auth D], I [auth M]	120	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B [auth A], F [auth C], G [auth B]	522	Influenza B virus (B/Lee/1940)	Mutation(s): 0  Gene Names: HA
Glycosylation
Glycosylation Sites: 2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
KL-BHA-4C2 light chain	C [auth L], D [auth N], E	111	Mus musculus	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth F], L [auth I], N [auth K]	3		N-Glycosylation

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth G], M [auth J], O	2		N-Glycosylation

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.61 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-08-26 
Deposition Author(s): Civljak, A., Bonnettaz, B., Bajic, G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI117287
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI109946
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI097092
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201400008C
Other private	United States	--

Revision History  

• Version 1.0: 2026-08-26
  Type: Initial release