8VEV

Structure of a mouse IgG antibody antigen-binding fragment (Fab) targeting N6-methyladenosine (m6A), an RNA modification, m6A nucleoside ligand

8VEV の概要

• エントリーDOI: 10.2210/pdb8vev/pdb
• 関連するPDBエントリー: 8SIP 8TCA
• 分子名称: N6-methyladenosine (m6A) binding IgG Fab, heavy chain, N6-methyladenosine (m6A) binding IgG Fab, light chain, DI(HYDROXYETHYL)ETHER, ... (7 entities in total)
• 機能のキーワード: igg fab, n6-methyladenosine (m6a), rna binding protein (rbp), modified rna, small molecule ligand, immune system
• 由来する生物種: Mus musculus; 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 143053.49

構造登録者

Aoki, S.T. (登録日: 2023-12-20, 公開日: 2024-02-07, 最終更新日: 2025-08-20)

主引用文献

Angelo, M.,Zhang, W.,Vilseck, J.Z.,Aoki, S.T.
In silico lambda-dynamics predicts protein binding specificities to modified RNAs.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: RNA modifications shape gene expression through a variety of chemical changes to canonical RNA bases. Although numbering in the hundreds, only a few RNA modifications are well characterized, in part due to the absence of methods to identify modification sites. Antibodies remain a common tool to identify modified RNA and infer modification sites through straightforward applications. However, specificity issues can result in off-target binding and confound conclusions. This work utilizes in silico λ-dynamics to efficiently estimate binding free energy differences of modification-targeting antibodies between a variety of naturally occurring RNA modifications. Crystal structures of inosine and N6-methyladenosine (m6A) targeting antibodies bound to their modified ribonucleosides were determined and served as structural starting points. λ-Dynamics was utilized to predict RNA modifications that permit or inhibit binding to these antibodies. In vitro RNA-antibody binding assays supported the accuracy of these in silico results. High agreement between experimental and computed binding propensities demonstrated that λ-dynamics can serve as a predictive screen for antibody specificity against libraries of RNA modifications. More importantly, this strategy is an innovative way to elucidate how hundreds of known RNA modifications interact with biological molecules without the limitations imposed by in vitro or in vivo methodologies.

PubMed: 40066880
DOI: 10.1093/nar/gkaf166

実験手法

X-RAY DIFFRACTION (3.06 Å)