9Y41 | pdb_00009y41

Crystal structure of hemagglutinin head domain from H1N1 Influenza A virus A/Victoria/2570/2019 bound to the 49_C09 antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 
    0.283 (Depositor), 0.283 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.238 (Depositor) 

Starting Models: experimental, in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9Y41

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: 144.24 kDa 
  • Atom Count: 9,937 
  • Modeled Residue Count: 1,301 
  • Deposited Residue Count: 1,330 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HemagglutininA [auth G],
B [auth C]
223Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A6M4YP75 (Influenza A virus)
Explore A0A6M4YP75 
Go to UniProtKB:  A0A6M4YP75
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6M4YP75
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Antibody 49_C09 heavy chainC [auth H],
E [auth A]
228Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Antibody 49_C09 light chainD [auth L],
F [auth B]
214Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free:  0.283 (Depositor), 0.283 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.238 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.351α = 90
b = 256.212β = 99.68
c = 61.773γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



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