8ATH

CRYSTAL STRUCTURE OF LAMP1 IN COMPLEX WITH FAB-B.

Summary for 8ATH

• Entry DOI: 10.2210/pdb8ath/pdb
• Descriptor: Lysosome-associated membrane glycoprotein 1, Fab B Heavy Chain, Fab B Light Chain, ... (4 entities in total)
• Functional Keywords: antigen, fab, complex, protein binding
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 6
• Total formula weight: 134706.15

Authors

Mathieu, M.,Dupuy, A. (deposition date: 2022-08-23, release date: 2023-03-01, Last modification date: 2024-10-23)

Primary citation

Pruvost, T.,Mathieu, M.,Dubois, S.,Maillere, B.,Vigne, E.,Nozach, H.
Deciphering cross-species reactivity of LAMP-1 antibodies using deep mutational epitope mapping and AlphaFold.
Mabs, 15:2175311-2175311, 2023

PubMed Abstract: Delineating the precise regions on an antigen that are targeted by antibodies has become a key step for the development of antibody therapeutics. X-ray crystallography and cryogenic electron microscopy are considered the gold standard for providing precise information about these binding sites at atomic resolution. However, they are labor-intensive and a successful outcome is not guaranteed. We used deep mutational scanning (DMS) of the human LAMP-1 antigen displayed on yeast surface and leveraged next-generation sequencing to observe the effect of individual mutants on the binding of two LAMP-1 antibodies and to determine their functional epitopes on LAMP-1. Fine-tuned epitope mapping by DMS approaches is augmented by knowledge of experimental antigen structure. As human LAMP-1 structure has not yet been solved, we used the AlphaFold predicted structure of the full-length protein to combine with DMS data and ultimately finely map antibody epitopes. The accuracy of this method was confirmed by comparing the results to the co-crystal structure of one of the two antibodies with a LAMP-1 luminal domain. Finally, we used AlphaFold models of non-human LAMP-1 to understand the lack of mAb cross-reactivity. While both epitopes in the murine form exhibit multiple mutations in comparison to human LAMP-1, only one and two mutations in the Macaca form suffice to hinder the recognition by mAb B and A, respectively. Altogether, this study promotes a new application of AlphaFold to speed up precision mapping of antibody-antigen interactions and consequently accelerate antibody engineering for optimization.

PubMed: 36797224
DOI: 10.1080/19420862.2023.2175311

Experimental method

X-RAY DIFFRACTION (2.366 Å)