8VK1

X-ray crystal structure of human IgE 4C8 Fab complex with Der p 2.0103


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.197 

wwPDB Validation   3D Report Full Report


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Literature

Structural analysis of human IgE monoclonal antibody epitopes on dust mite allergen Der p 2.

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

(2024) J Allergy Clin Immunol 

  • DOI: https://doi.org/10.1016/j.jaci.2024.04.017
  • Primary Citation of Related Structures:  
    8VK1, 8VK2

  • PubMed Abstract: 

    Human IgE (hIgE) mAbs against major mite allergen Der p 2 developed using human hybridoma technology were used for IgE epitope mapping and analysis of epitopes associated with the hIgE repertoire. We sought to elucidate the new hIgE mAb 4C8 epitope on Der p 2 and compare it to the hIgE mAb 2F10 epitope in the context of the allergenic structure of Der p 2. X-ray crystallography was used to determine the epitope of anti-Der p 2 hIgE mAb 4C8. Epitope mutants created by targeted mutagenesis were analyzed by immunoassays and in vivo using a human high-affinity IgE receptor (FcεRIα)-transgenic mouse model of passive systemic anaphylaxis. The structure of recombinant Der p 2 with hIgE mAb 4C8 Fab was determined at 3.05 Å. The newly identified epitope region does not overlap with the hIgE mAb 2F10 epitope or the region recognized by 3 overlapping hIgE mAbs (1B8, 5D10, and 2G1). Compared with wild-type Der p 2, single or double 4C8 and 2F10 epitope mutants bound less IgE antibodies from allergic patients by as much as 93%. Human FcεRIα-transgenic mice sensitized by hIgE mAbs, which were susceptible to anaphylaxis when challenged with wild-type Der p 2, could no longer cross-link FcεRI to induce anaphylaxis when challenged with the epitope mutants. These data establish the structural basis of allergenicity of 2 hIgE mAb nonoverlapping epitopes on Der p 2, which appear to make important contributions to the hIgE repertoire against Der p 2 and provide molecular targets for future design of allergy therapeutics.


  • Organizational Affiliation

    InBio, Charlottesville, Va. Electronic address: aball@inbio.com.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IgE 4C8 light chainA [auth E],
D [auth B]
212Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Der p 2 variant 3B [auth D],
F [auth A]
129Dermatophagoides pteronyssinusMutation(s): 0 
UniProt
Find proteins for I2CMD6 (Dermatophagoides pteronyssinus)
Explore I2CMD6 
Go to UniProtKB:  I2CMD6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI2CMD6
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
IgE 4C8 heavy chainC [auth F],
E [auth C]
232Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 225.254α = 90
b = 95.298β = 105.724
c = 69.209γ = 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 StatesR01 AI077653

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release