9NJ3 | pdb_00009nj3

Computationally optimized broadly reactive influenza B hemagglutinin BC2 bound by antibodies #46 and #3978

• PDB DOI: https://doi.org/10.2210/pdb9NJ3/pdb
• EM Map EMD-49463: EMDB EMDataResource

• Classification: VIRAL PROTEIN/Immune System
• Organism(s): Influenza B virus, Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2025-02-26 Released: 2026-03-11 
• Deposition Author(s): Dzimianski, J.V., Kunkel, I., Balasco Serrao, V.H., DuBois, R.M.
• 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: 2.48 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Computationally optimized broadly reactive influenza B hemagglutinin BC2 bound by antibodies #46 and #3978

Dzimianski, J.V., Kunkel, I., Balasco Serrao, V.H., DuBois, R.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A3B2C2D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A6B3 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 320.3 kDa 
• Atom Count: 11,862 
• Modeled Residue Count: 1,540 
• Deposited Residue Count: 2,953 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, B, C	530	Influenza B virus	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for P17504 (Influenza B virus (strain B/Beijing/1/1987)) Explore P17504  Go to UniProtKB:  P17504
Glycosylation
Glycosylation Sites: 4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab A Heavy Chain	D [auth H], E [auth J]	239	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab A Light Chain	F [auth K], G [auth L]	217	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab B Heavy Chain	H [auth Q]	233	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab B Light Chain	I [auth P]	218	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth D], K [auth E], M [auth G]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	L [auth F], N [auth I]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	O [auth A], P [auth C], Q [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.48 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.5.3
MODEL REFINEMENT	PHENIX	1.21.2_5419
MODEL REFINEMENT	ISOLDE
MODEL REFINEMENT	Coot

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-03-11 
Deposition Author(s): Dzimianski, J.V., Kunkel, I., Balasco Serrao, V.H., DuBois, R.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93019C00052

Revision History  

• Version 1.0: 2026-03-11
  Type: Initial release