9NPI | pdb_00009npi

X-ray crystal structure of recombinant Can f 1 in complex with human IgE 12F3 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.226 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.187 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Human IgE monoclonal antibodies define two unusual epitopes trapping dog allergen Can f 1 in different conformations.

Khatri, K.Ball, A.Glesner, J.Linn, C.Vailes, L.D.Wunschmann, S.Gabel, S.A.Zhang, J.Peebles Jr., R.S.Borowski, T.Mueller, G.A.Chapman, M.D.Smith, S.A.Pomes, A.Chruszcz, M.

(2025) Protein Sci 34: e70269-e70269

  • DOI: https://doi.org/10.1002/pro.70269
  • Primary Citation of Related Structures:  
    8VQF, 8VQG, 9NPG, 9NPH, 9NPI

  • PubMed Abstract: 

    Molecular analysis of interactions between IgE antibody and allergen allows the structural basis of IgE recognition to be defined. Human IgE (hIgE) epitopes of respiratory lipocalin allergens, including Can f 1, remain elusive due to a lack of IgE-allergen complexes. This study aims to map the structure of allergenic epitopes on Can f 1. The fragment antigen-binding (Fab) regions of Can f 1 specific human IgE monoclonal antibodies (hIgE mAb) were used to determine the structures of IgE epitopes. Epitope mutants were designed to target Can f 1 epitopes. Immunoassays and a human FcεRIα transgenic mouse model of passive anaphylaxis in vivo were used to assess the functional activity of epitope mutants. Crystal structures of natural or recombinant Can f 1 complexed with two hIgE mAb 1J11 and 12F3 Fabs, respectively, were determined. The hIgE mAb bound to two partially overlapping epitopes and recognized two different Can f 1 conformations. The hIgE mAb 12F3 showed an unusual mode of binding by protruding its heavy chain CDR3 inside the Can f 1 calyx. Epitope mutants generated based on the structural analyses displayed a 64%-89% reduction in IgE antibody binding and failed to induce passive anaphylaxis in a human FcεRIα transgenic mouse model. In summary, the structures of Can f 1-hIgE Fab complexes revealed two unique and partially overlapping epitopes on Can f 1. The modification of the identified IgE epitopes provides a pathway for the design of hypoallergens to treat dog allergies.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Human IgE 12F3 heavy chainA [auth C]225Homo sapiensMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Human IgE 12F3 light chain215Homo sapiensMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Major allergen Can f 1C [auth A]156Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for O18873 (Canis lupus familiaris)
Explore O18873 
Go to UniProtKB:  O18873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO18873
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.226 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.187 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.528α = 90
b = 73.95β = 99.588
c = 77.275γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI077653-14

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release