EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	Small siphophage binding to an open state of the LptDE outer membrane lipopolysaccharide translocon.
ジャーナル・号・ページ	Proc Natl Acad Sci U S A, Vol. 122, Issue 48, Page e2516650122, Year 2025
掲載日	2025年12月2日
著者	Emily Dunbar / Robert Clark / Arnaud Baslé / Shenaz Allyjaun / Hector Newman / Julia Hubbard / Syma Khalid / Bert van den Berg /
PubMed 要旨	Bacteriophages are bacterial viruses that provide alternatives to small-molecule drugs to combat infections by antibiotic-resistant bacteria. To infect a bacterial host, a phage needs to bind to the ...Bacteriophages are bacterial viruses that provide alternatives to small-molecule drugs to combat infections by antibiotic-resistant bacteria. To infect a bacterial host, a phage needs to bind to the bacterial surface via receptor binding proteins (RBPs), which are critical for determining host specificity. For functionally important receptors, the RBP-receptor interaction could be exploited via phage steering, where emerging bacterial resistance due to receptor modification could make bacteria less fit or virulent. Despite this, relatively little is known about RBP-receptor interactions. Here, we build on the recent discovery of coliphages that have the outer membrane (OM) lipopolysaccharide translocon LptDE as their terminal receptor and show via cryogenic electron microscopy that, surprisingly, the RBP of the small siphophage Oekolampad binds to a hitherto unobserved, open state of LptDE. The open lateral gate of LptD is occupied by a β-strand peptide originating from the degraded N-terminal jellyroll domain of LptD, suggesting the possibility of LptD inhibition via peptidomimetics. A structure of LptDE in complex with the superinfection exclusion (SE) protein Rtp45 of the Oekolampad-related phage Rtp shows a mechanism of SE where Rtp45-induced conformational changes in LptD resulting from steric clashes preclude RBP binding. Finally, analysis of spontaneous Oekolampad-resistant mutants identifies mutations in LptD that abolish the LptDE-RBP interaction in vitro. SDS-EDTA sensitivity assays of the mutants show no major OM defects, consistent with largely preserved LptDE function, and suggesting that phage steering via LptDE might be challenging.
リンク	Proc Natl Acad Sci U S A / PubMed:41296721 / PubMed Central
手法	EM (単粒子)
解像度	2.76 - 3.2 Å
構造データ	54169 9rpr EMDB-54169, PDB-9rpr: Cryo-EM structure of LptDEM complex containing Shigella flexneri LptE and endogenous E. coli LptD and LptM 手法: EM (単粒子) / 解像度: 2.78 Å 54170 9rps EMDB-54170, PDB-9rps: Cryo-EM structure of Shigella flexneri LptDE in complex with RTP45 superinfection exclusion protein from RTP bacteriophage and endogenous LptM 手法: EM (単粒子) / 解像度: 3.01 Å 54171 9rpt EMDB-54171, PDB-9rpt: Cryo-EM structure of the open state of Shigella flexneri LptDE bound by the RBP of Oekolampad phage 手法: EM (単粒子) / 解像度: 2.81 Å 54173 9rpw EMDB-54173, PDB-9rpw: Cryo-EM structure of Shigella flexneri LptDE dimer: closed-state unbound and open-state bound by Oekolampad phage RBP 手法: EM (単粒子) / 解像度: 3.2 Å 54175 9rqi EMDB-54175, PDB-9rqi: Cryo-EM structure of Shigella flexneri LptDE bound by phage RBP reveals N-terminal strand insertion into lateral gate 手法: EM (単粒子) / 解像度: 2.76 Å
化合物	ChemComp-PLM: PALMITIC ACID ChemComp-PXS: (2S)-propane-1,2-diyl dihexadecanoate
由来	shigella flexneri (フレクスナー赤痢菌) escherichia coli (大腸菌) escherichia phage rtp (ファージ) escherichia phage oekolampad (ファージ)
キーワード	MEMBRANE PROTEIN / lipopolysaccharide transport / outer membrane protein complex / beta-barrel / lipoprotein / outer membrane complex / superinfection exclusion / bacteriophage / receptor-binding protein