8PKC image
Deposition Date 2023-06-26
Release Date 2024-05-08
Last Version Date 2026-07-01
Entry Detail
PDB ID:
8PKC
Keywords:
Title:
Structure of Api m1 in complex with the AM1-4 nanobody
Biological Source:
Source Organism(s):
Lama glama (Taxon ID: 9844)
Apis mellifera (Taxon ID: 7460)
Expression System(s):
Method Details:
Experimental Method:
Resolution:
4.10 Å
R-Value Free:
0.29
R-Value Work:
0.25
R-Value Observed:
0.26
Space Group:
P 41 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Phospholipase A2
Chain IDs:A, B
Chain Length:134
Number of Molecules:2
Biological Source:Apis mellifera
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:AM1-4 nanobody
Chain IDs:C, D
Chain Length:129
Number of Molecules:2
Biological Source:Lama glama
Ligand Molecules
Primary Citation
Nanobody-based IgG simultaneously inhibit the allergenic and enzymatic activity of the dominant honeybee venom allergen.
Nat Commun 17 1814 1814 (2026)
PMID: 41702899 DOI: 10.1038/s41467-026-69572-0

Abstact

Insect venoms can cause severe allergic reactions, including anaphylaxis, in sensitized individuals. In this study, we aim at preventing anaphylaxis mediated by the most abundant and dominant honeybee venom allergen phospholipase A2 (Api m 1) by blocking its interaction with allergic patient IgE. Therefore, we characterize selected Api m 1-specific nanobodies and identify two high-affinity binders with non-overlapping epitopes. Crystal structures of Api m 1/nanobody complexes reveal diametrically opposed epitopes, one of which involves the active site of Api m 1. Based on this background, we develop mono- and bispecific nanobody-human IgG(1) Fc, which exhibits pronounced blocking of IgE binding and effector cell activation in blood samples from honeybee venom allergic patients and reduces systemic reactions in a mouse model of allergen-induced anaphylaxis. This work provides a rationale for using nanobody-based inhibitors to prevent Api m 1-mediated anaphylaxis in honeybee venom allergy.

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Primary Citation of related structures
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