Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Small siphophage binding to an open state of the LptDE outer membrane lipopolysaccharide translocon.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 122, Issue 48, Page e2516650122, Year 2025
Publish date	Dec 2, 2025
Authors	Emily Dunbar / Robert Clark / Arnaud Baslé / Shenaz Allyjaun / Hector Newman / Julia Hubbard / Syma Khalid / Bert van den Berg /
PubMed Abstract	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.
External links	Proc Natl Acad Sci U S A / PubMed:41296721 / PubMed Central
Methods	EM (single particle)
Resolution	2.76 - 3.2 Å
Structure data	54169 9rpr EMDB-54169, PDB-9rpr: Cryo-EM structure of LptDEM complex containing Shigella flexneri LptE and endogenous E. coli LptD and LptM Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 2.76 Å
Chemicals	ChemComp-PLM: PALMITIC ACID ChemComp-PXS: (2S)-propane-1,2-diyl dihexadecanoate
Source	shigella flexneri (bacteria) escherichia coli (E. coli) escherichia phage rtp (virus) escherichia phage oekolampad (virus)
Keywords	MEMBRANE PROTEIN / lipopolysaccharide transport / outer membrane protein complex / beta-barrel / lipoprotein / outer membrane complex / superinfection exclusion / bacteriophage / receptor-binding protein