9CMC | pdb_00009cmc

Crystal structure of the peanut allergen Ara h 2 with two human derived Fab antibodies 22S1 and 23P34


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 
    0.253 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Germline-encoded recognition of peanut underlies development of convergent antibodies in humans.

Marini-Rapoport, O.Andrieux, L.Keswani, T.Zong, G.Duchen, D.Yaari, G.Min, J.Lytle, I.R.Rosenberg, A.F.Fucile, C.Kobie, J.J.Piepenbrink, M.S.Sun, T.Martin, V.M.Yuan, Q.Shreffler, W.G.Seppo, A.E.Jarvinen, K.M.Loeffler, J.R.Ward, A.B.Kleinstein, S.H.Pedersen, L.C.Fernandez-Quintero, M.L.Mueller, G.A.Patil, S.U.

(2025) Sci Transl Med 17: eadw4148-eadw4148

  • DOI: https://doi.org/10.1126/scitranslmed.adw4148
  • Primary Citation of Related Structures:  
    9CMC

  • PubMed Abstract: 

    Humans develop immunoglobulin G (IgG) antibodies to the foods they consume. In the context of food allergy, allergen-specific IgG antibodies can sequentially class-switch to pathogenic IgE. However, the mechanism underlying the antigenicity of food proteins remains uncharacterized. Here, we identified convergent antibodies arising from different antibody gene rearrangements that bind to the immunodominant peanut allergen Ara h 2 and characterized allelic and junctional constraints on germline antibody specificity. Structurally, we found similar epitope-paratope interactions across multiple gene rearrangements. We demonstrate that these germline-encoded epitope-specific convergent antibodies to peanut occur commonly in the population because of the worldwide prevalence of the relevant gene rearrangements, allelic independence, and junctional malleability. As a result, serum IgG to this public epitope is prevalent among diverse cohorts of nonallergic peanut-consuming infants and peanut-allergic children and adults. This work demonstrates that IgG recognition of dietary antigens can be intrinsically programmed by the germline antibody repertoire.


  • Organizational Affiliation

    Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA 02124, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 23P34 heavy chain
A, F, K, P
225Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 23P34 light chain
B, G, L, Q
218Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 22S1 heavy chain
C, H, M, R
228Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 22S1 light chainD,
I,
N,
S [auth V]
214Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ara h 2 allergen
E, J, O, T
140Arachis hypogaeaMutation(s): 0 
Gene Names: Ara h 2Ahy_A08g040012
UniProt
Find proteins for A0A445BYI5 (Arachis hypogaea)
Explore A0A445BYI5 
Go to UniProtKB:  A0A445BYI5
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UniProt GroupA0A445BYI5
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free:  0.253 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.906α = 90
b = 165.009β = 105.93
c = 164.642γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZIC ES102645
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZIA ES102906

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release
  • Version 1.1: 2025-06-25
    Changes: Database references