9KKJ

Structure of Nectin-4 D1 domain in complex with the Fab fragment of 9MW2821 mAb

9KKJ の概要

• エントリーDOI: 10.2210/pdb9kkj/pdb
• EMDBエントリー: 62389
• 分子名称: 9MW2821 mAb Fab Light chain, 9MW2821 mAb Fab Heavy Chain, Nectin-4 (3 entities in total)
• 機能のキーワード: antibody-antigen complex, immune system
• 由来する生物種: Mus musculus; 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 59564.62

構造登録者

Wen, H.Y. (登録日: 2024-11-13, 公開日: 2025-11-19, 最終更新日: 2025-11-26)

主引用文献

Fang, P.,You, M.,Wen, H.,Cao, Y.,Zhou, W.,Zhu, X.,Shi, L.,Sun, X.,Li, K.,Li, W.,Wang, J.,Wu, H.,Tan, X.
Structural basis of nectin-4 recognition by the antibody-drug conjugate 9MW2821.
J.Biol.Chem., 301:110816-110816, 2025

PubMed Abstract: Nectin-4, a membrane protein highly expressed in multiple solid tumors, has become an attractive target for antibody-drug conjugate development. We designed and developed 9MW2821, an anti-nectin-4 antibody-drug conjugate with an enzymatically cleavable valine-citrulline linker and monomethyl auristatin E as the payload. Although 9MW2821 has shown good efficacy and safety in multiple solid tumors in clinical trials, the interaction between 9MW2821 and nectin-4 at the molecular level remains unclear. In this study, we solved the structure of the antigen-binding fragment of 9MW2821 in complex with nectin-4 at a resolution of 3.26 Å using single-particle cryo-EM. The structure shows that 9MW2821 binds the front β-sheet of nectin-4 D1 through three complementarity-determining region loops from the heavy chain and two complementarity-determining region loops from the light chain. The binding involves extensive hydrogen bonds and hydrophobic interactions. The buried surface area is more than 1600 Å. Mutagenesis studies revealed that four residues (Q77, E78, H83, and E95) of nectin-4 contributed significantly to the binding of 9MW2821 monoclonal antibody (mAb). The structure also shows that 9MW2821 mAb blocks nectin-4 homodimer formation by competing with the nectin-4 partner D1 domain for part of the nectin-4 surface area. Furthermore, 9MW2821 mAb prevents nectin-4 from interacting with nectin-1 and T-cell immunoglobulin and immunoreceptor tyrosine-based inhibitory motif domain, enhancing the activation of NK cells. Based on the structure of the nectin-4 D1-9MW2821 antigen-binding fragment complex resolved in this study, we have elucidated the molecular mechanism of 9MW2821 in cancer therapy. The findings provide a basis for optimizing future mAbs targeting nectin-4.

PubMed: 41101504
DOI: 10.1016/j.jbc.2025.110816

実験手法

ELECTRON MICROSCOPY (3.26 Å)