9Y3Z | pdb_00009y3z

Crystal structure of hemagglutinin head domain from H3N2 Influenza A virus A/New York/631/1996 bound to the 3_H2 antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.226 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Models: experimental, in silico
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

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

  • 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.


  • Organizational Affiliation
    • Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.

Macromolecule Content 

  • Total Structure Weight: 78.41 kDa 
  • Atom Count: 5,931 
  • Modeled Residue Count: 700 
  • Deposited Residue Count: 707 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin266Influenza 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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1PT16
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Antibody 3_H2 heavy chainB [auth H]225Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Antibody 3_H2 light chainC [auth L]216Homo sapiensMutation(s): 0 

Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth C]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.226 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.767α = 90
b = 123.089β = 90
c = 144.423γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States75N93021C00015

Revision History  (Full details and data files)

  • 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