9FZD

Structure of OmpA-long in complex with nanobody Nb39

9FZD の概要

• エントリーDOI: 10.2210/pdb9fzd/pdb
• 分子名称: Outer membrane protein A, Nanobody 39 (3 entities in total)
• 機能のキーワード: porin, nanobody, complex, membrane protein
• 由来する生物種: Escherichia coli; 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 32474.16

構造登録者

Ackle, F.,Sorgenfrei, M.,Seeger, M.A. (登録日: 2024-07-05, 公開日: 2024-07-17, 最終更新日: 2025-07-23)

主引用文献

Sorgenfrei, M.,Hurlimann, L.M.,Printz, A.,Wegner, F.,Morger, D.,Ackle, F.,Remy, M.M.,Montowski, G.,Keserue, H.A.,Cuenod, A.,Imkamp, F.,Egli, A.,Keller, P.M.,Seeger, M.A.
Rapid detection and capture of clinical Escherichia coli strains mediated by OmpA-targeting nanobodies.
Commun Biol, 8:1047-1047, 2025

PubMed Abstract: Escherichia coli is a major cause of blood stream and urinary tract infections. Owing to the spread of antimicrobial resistance, it is often treated with an inadequate antibiotic. With the aim to accelerate the diagnostics of this key pathogen, we used the flycode technology to generate nanobodies against the conserved and highly abundant outer membrane protein OmpA. Two nanobodies each recognizing a different isoform of OmpA were shown by flow cytometry to recognize > 91% of 85,680 E. coli OmpA sequences deposited in a large bacterial genome database. Crystal structures of these nanobodies in complex with the respective OmpA isoform revealed interactions with all four surface accessible loops of OmpA. Steric hindrance caused by dense O-antigen layers initially impeded reliable capture of clinical E. coli strains. By generating nanobody constructs with long linkers and by thinning the O-antigen layer through alterations to growth medium and buffers, we achieved to capture < 50 CFU/mL. Our work provides a framework to generate nanobodies for the specific and sensitive detection and capture of clinically relevant pathogenic bacteria.

PubMed: 40659774
DOI: 10.1038/s42003-025-08345-9

実験手法

X-RAY DIFFRACTION (2.3 Å)