9NCD image
Deposition Date 2025-02-15
Release Date 2026-02-18
Last Version Date 2026-02-18
Entry Detail
PDB ID:
9NCD
Keywords:
Title:
Crystal structure of the peanut allergen Ara h 9 with bound Fab IGX-3103 and antiFab nanobody
Biological Source:
Source Organism(s):
Homo sapiens (Taxon ID: 9606)
Lama glama (Taxon ID: 9844)
Arachis hypogaea (Taxon ID: 3818)
Expression System(s):
Method Details:
Experimental Method:
Resolution:
1.60 Å
R-Value Free:
0.19
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Non-specific lipid-transfer protein
Chain IDs:D (auth: A)
Chain Length:93
Number of Molecules:1
Biological Source:Arachis hypogaea
Polymer Type:polypeptide(L)
Molecule:Fab IGX-3103 heavy chain
Chain IDs:B (auth: H)
Chain Length:451
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:anti Kappa light chain nanobody (antiFab)
Chain IDs:C (auth: K)
Chain Length:123
Number of Molecules:1
Biological Source:Lama glama
Polymer Type:polypeptide(L)
Molecule:Fab IGX-3103 light chain
Chain IDs:A (auth: L)
Chain Length:214
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation

Abstact

BACKGROUND AND OBJECTIVES Nonspecific lipid transfer proteins (nsLTPs) are frequently cross-reactive allergens that hamper diagnosis and avoidance. It is challenging to distinguish cross-reactivity from cosensitization with polyclonal serum owing to the presence of a few promiscuous antibodies or many highly specific antibodies. Objective: We hypothesized that a robust analysis of more human monoclonal antibodies (mAbs) would enable us to compare crossreactivity with cosensitization. METHODS Human monoclonal antibodies were cloned from allergic patients via single cell sequencing and screened for affinity to extracts and recombinant allergens. Ara h 9 was expressed and crystallized with the mAb IGX-3103. Affinity for nsLTPs was explored using molecular modeling, site-directed mutagenesis, and ELISA. RESULTS A human IgG4 mAb named IGX-3103 was discovered from a type 2-polarized memory B cell expressing CD23, IL-4Ra, and germline IGHE. IGX-3103 bound to 19 different type 1 nsLTP allergens and to extracts from sources without a characterized nsLTP allergen. The structure showed that IGX-3103 induced a conformational change in Ara h 9, enabling a hydrophobic residue from the antibody, Phe104, to enter the lipid binding cavity. Key residues in the epitope were identified to include Leu1, Ser2, Cys3, Lys39, and Asp43 in Ara h 9; these residues are conserved across type 1 nsLTPs, thus explaining the promiscuity of IGX-3103. CONCLUSIONS IGX-3103 is an example of a human mAb with cross-reactivity to pollen, fruit, and seed type 1 nsLTPs. This observation anecdotally supports the possibility that a few promiscuous mAbs could be driving cross-reactivity.

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