9Y40 | pdb_00009y40

Crystal structure of hemagglutinin head domain from H3N2 Influenza A virus A/New York/631/1996 bound to the 49_C09 antibody

• PDB DOI: https://doi.org/10.2210/pdb9Y40/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Influenza A virus (A/New York/631/1996(H3N2)), Homo sapiens
• Expression System: Trichoplusia ni, Homo sapiens
• Mutation(s): No 


• Deposited: 2025-09-02 Released: 2026-05-06 
• Deposition Author(s): Wang, B., Wilson, I.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.71 Å
• R-Value Free: 
  0.238 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Models: experimental, in silico

Literature

Childhood immunological imprinting of cross-subtype antibodies targeting the hemagglutinin head domain of influenza viruses.

Li, S.H., Wang, B., Jo, G., Mikelov, A., Atkinson, R.K., Le Sage, V., Furey, C., Ort, J.T., Ye, N., Gang, S., Shah, R., Santos, J.J.S., Roltgen, K., Joshi, S.A., Lee, J.Y., Pursell, T.A., Drapeau, E.M., Han, J., Callear, A.P., Collman, R.G., Monto, A.S., Martin, E.T., Lakdawala, S.S., Ward, A.B., Wilson, I.A., Boyd, S.D., Hensley, S.E.

(2026) Cell Host Microbe 34: 873-887.e11

• PubMed: 42049037 
• DOI: https://doi.org/10.1016/j.chom.2026.04.004
• Primary Citation Related Structures: 
  9Y3X, 9Y3Y, 9Y3Z, 9Y40, 9Y41


• PubMed Abstract: 
  

  Influenza virus cross-subtype antibodies targeting epitopes in the hemagglutinin (HA) head are rare because these epitopes are variable between influenza virus subtypes. We found that a large proportion of monoclonal antibodies (mAbs) isolated from individuals immunized with the 2021-22 seasonal influenza vaccine bound to an epitope on the HA head of both the H1N1 vaccine strain and H3N2 strains from the mid-1990s. The unmutated common ancestors of many of these mAbs reacted to both the 1990s H3s and the 2021-22 H1 vaccine strain. These cross-subtype antibodies were also found in polyclonal sera, but only among individuals born in the 1990s. Ferrets sequentially exposed to a 1990s H3N2 virus and contemporary influenza vaccine also produced H1/H3 cross-reactive antibodies. Recently, H1N1 viruses have acquired a substitution that abrogates the binding of these antibodies. Together, our study demonstrates how prior influenza virus exposures can influence the specificity of antibodies elicited by entirely different influenza virus subtypes.

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Organizational Affiliation: 
• Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Department of Pathology, Stanford University School of Medicine, Stanford, CA 94304, USA.
Center for Vaccine Research and Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA.
Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: [e-mail].
Department of Pathology, Stanford University School of Medicine, Stanford, CA 94304, USA. Electronic address: [e-mail].
Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 77.2 kDa 
• Atom Count: 5,356 
• Modeled Residue Count: 699 
• Deposited Residue Count: 710 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A	268	Influenza A virus (A/New York/631/1996(H3N2))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for Q1PT16 (Influenza A virus) Explore Q1PT16  Go to UniProtKB:  Q1PT16
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody 49_C09 heavy chain	B [auth H]	228	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody 49_C09 light chain	C [auth L]	214	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.71 Å
• R-Value Free:  0.238 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.358	α = 90
b = 170.358	β = 90
c = 95.831	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Currently 9Y40 does not have a validation slider image.

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-06 
Deposition Author(s): Wang, B., Wilson, I.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93021C00015

Revision History  

• Version 1.0: 2026-05-06
  Type: Initial release
  
• Version 1.1: 2026-05-13
  Changes: Database references
• Version 1.2: 2026-05-20
  Changes: Database references