8PKC | pdb_00008pkc

Structure of Api m1 in complex with the AM1-4 nanobody

• PDB DOI: https://doi.org/10.2210/pdb8PKC/pdb

• Classification: ALLERGEN
• Organism(s): Apis mellifera, Lama glama
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-26 Released: 2024-05-08 
• Deposition Author(s): Aagaard, J.B., Gandini, R., Spillner, E., Miehe, M.
• Funding Organization(s): Danish Council for Independent Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.10 Å
• R-Value Free: 
  0.296 (Depositor), 0.295 (DCC) 
• R-Value Work: 
  0.258 (Depositor), 0.258 (DCC) 
• R-Value Observed: 
  0.262 (Depositor) 

Starting Model: experimental

Literature

Nanobody-based IgG simultaneously inhibit the allergenic and enzymatic activity of the dominant honeybee venom allergen.

Aagaard, J.B., Gandini, R., Ballegaard, A.R., Jensen, B.K., Dorn, B., Larsen, A.V.B., Lenstrup, A., Sonderholm, M., Miehe, M., Pfutzner, W., Jakob, T., Andersen, G.R., Mobs, C., Spillner, E.

(2026) Nat Commun 17: 1814-1814

• PubMed: 41702899 
• DOI: https://doi.org/10.1038/s41467-026-69572-0
• Primary Citation Related Structures: 
  8PIH, 8PKC


• PubMed Abstract: 
  

  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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Organizational Affiliation: 
• Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark.
Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
Department of Dermatology and Allergology, Justus Liebig University Giessen, Giessen, Germany.
Department of Dermatology and Allergology, Clinical & Experimental Allergology, Philipps University Marburg, Marburg, Germany.
Department of Dermatology and Allergology, Justus Liebig University Giessen, Giessen, Germany. [e-mail].
Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark. [e-mail].
Department of Dermatology and Allergology, Clinical & Experimental Allergology, Philipps University Marburg, Marburg, Germany. [e-mail].
Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 58.58 kDa 
• Atom Count: 4,065 
• Modeled Residue Count: 522 
• Deposited Residue Count: 526 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2	A, B	134	Apis mellifera	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for P00630 (Apis mellifera) Explore P00630  Go to UniProtKB:  P00630
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AM1-4 nanobody	C, D	129	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	E [auth A], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.10 Å
• R-Value Free:  0.296 (Depositor), 0.295 (DCC) 
• R-Value Work:  0.258 (Depositor), 0.258 (DCC) 
• R-Value Observed: 0.262 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.6	α = 90
b = 93.6	β = 90
c = 189.49	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-08 
Deposition Author(s): Aagaard, J.B., Gandini, R., Spillner, E., Miehe, M.

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Funding Organization	Location	Grant Number
Danish Council for Independent Research	Denmark	0135-00061B

Revision History  

• Version 1.0: 2024-05-08
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary
• Version 1.2: 2026-07-01
  Changes: Database references