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	The proline-rich antimicrobial peptide Api137 disrupts large ribosomal subunit assembly and induces misfolding.
Journal, issue, pages	Nat Commun, Vol. 16, Issue 1, Page 567, Year 2025
Publish date	Jan 10, 2025
Authors	Simon Malte Lauer / Jakob Gasse / Andor Krizsan / Maren Reepmeyer / Thiemo Sprink / Rainer Nikolay / Christian M T Spahn / Ralf Hoffmann /
PubMed Abstract	The proline-rich antimicrobial designer peptide Api137 inhibits protein expression in bacteria by binding simultaneously to the ribosomal polypeptide exit tunnel and the release factor (RF), ...The proline-rich antimicrobial designer peptide Api137 inhibits protein expression in bacteria by binding simultaneously to the ribosomal polypeptide exit tunnel and the release factor (RF), depleting the cellular RF pool and leading to ribosomal arrest at stop codons. This study investigates the additional effect of Api137 on the assembly of ribosomes using an Escherichia coli reporter strain expressing one ribosomal protein per 30S and 50S subunit tagged with mCherry and EGFP, respectively. Separation of cellular extracts derived from cells exposed to Api137 in a sucrose gradient reveals elevated levels of partially assembled and not fully matured precursors of the 50S subunit (pre-50S). High-resolution structures obtained by cryogenic electron microscopy demonstrate that a large proportion of pre-50S states are missing up to five proteins (uL22, bL32, uL29, bL23, and uL16) and have misfolded helices in 23S rRNA domain IV. These data suggest a second mechanism for Api137, wherein it disrupts 50S subunit assembly by inducing the formation of misfolded precursor particles potentially incapable of evolving into active ribosomes, suggesting a bactericidal mechanism.
External links	Nat Commun / PubMed:39794318 / PubMed Central
Methods	EM (single particle)
Resolution	2.98 - 7.06 Å
Structure data	51828 9h3k EMDB-51828, PDB-9h3k: 50S subunit precursor d126_(L29)-/(L22)- Method: EM (single particle) / Resolution: 6.62 Å 51829 9h3l EMDB-51829, PDB-9h3l: 50S subunit precursor C_(L29)-/(L22)- Method: EM (single particle) / Resolution: 5.84 Å 51830 9h3m EMDB-51830, PDB-9h3m: 50S subunit precursor C_(L22)- Method: EM (single particle) / Resolution: 4.41 Å 51831 9h3n EMDB-51831, PDB-9h3n: 50S subunit precursor C_(L22)-~H61 Method: EM (single particle) / Resolution: 3.69 Å 51832 9h3o EMDB-51832, PDB-9h3o: 50S subunit precursor C_(L22)-_GAC Method: EM (single particle) / Resolution: 4.54 Å 51833 9h3p EMDB-51833, PDB-9h3p: 50S subunit precursor C-CP_(L22)- Method: EM (single particle) / Resolution: 7.06 Å 51834 9h3q EMDB-51834, PDB-9h3q: 50S subunit precursor C-CP_YjgA_(L22)-~H61 Method: EM (single particle) / Resolution: 4.02 Å 51835 9h3r EMDB-51835, PDB-9h3r: 50S subunit precursor C-CP_YjgA_(L22)- Method: EM (single particle) / Resolution: 4.12 Å 51836 9h3s EMDB-51836, PDB-9h3s: 50S subunit precursor C-CP_YjgA_L22 Method: EM (single particle) / Resolution: 4.16 Å 51837 9h3t EMDB-51837, PDB-9h3t: 50S subunit precursor C_L2 Method: EM (single particle) / Resolution: 3.85 Å 51838 9h3u EMDB-51838, PDB-9h3u: 50S subunit precursor C_H68 Method: EM (single particle) / Resolution: 3.47 Å 51839 9h3v EMDB-51839, PDB-9h3v: 50S subunit precursor C-CP_L2-L28 Method: EM (single particle) / Resolution: 3.55 Å 51840 9h3w EMDB-51840, PDB-9h3w: 50S subunit precursor C-CP_H68 Method: EM (single particle) / Resolution: 5.38 Å 51841 9h3x EMDB-51841, PDB-9h3x: 50S subunit precursor C-CP_H68_L35 Method: EM (single particle) / Resolution: 4.12 Å 51842 9h3y EMDB-51842, PDB-9h3y: 50S subunit precursor 50S_(L16)- Method: EM (single particle) / Resolution: 3.09 Å 51843 9h3z EMDB-51843, PDB-9h3z: mature 50S subunit Method: EM (single particle) / Resolution: 2.98 Å 51973 9ha1 EMDB-51973, PDB-9ha1: Pooled 50S subunit C_(L22)- precursor states supplemented with Api137 - Canonical PET exit Api137 Method: EM (single particle) / Resolution: 4.17 Å 51974 9ha2 EMDB-51974, PDB-9ha2: Pooled 50S subunit C_(L22)- precursor states supplemented with Api137 - Alternative PET exit Api137 Method: EM (single particle) / Resolution: 4.17 Å 51975 9ha3 EMDB-51975, PDB-9ha3: Pooled 50S subunit C_(L22)-~H61 precursor states supplemented with Api137 Method: EM (single particle) / Resolution: 3.62 Å 51976 9ha4 EMDB-51976, PDB-9ha4: Pooled 50S subunit C-CP_(L22)- precursor states supplemented with Api137 Method: EM (single particle) / Resolution: 4.26 Å 51977 9ha5 EMDB-51977, PDB-9ha5: Pooled 50S subunit C_L2 precursor states supplemented with Api137 Method: EM (single particle) / Resolution: 3.3 Å 51978 9ha6 EMDB-51978, PDB-9ha6: mature 50S subunit supplemented with Api137 Method: EM (single particle) / Resolution: 3.08 Å 51979 9ha7 EMDB-51979, PDB-9ha7: Pooled 50S subunit C-CP_(L22)-~H61 precursor states supplemented with Api137 Method: EM (single particle) / Resolution: 4.37 Å 51981 9hai EMDB-51981, PDB-9hai: Pooled 50S subunit C-CP_L2-L28 precursor states supplemented with Api137 Method: EM (single particle) / Resolution: 3.01 Å 51982 9hal EMDB-51982, PDB-9hal: Pooled 50S subunit d126_(L29)-/(L22)- precursor states supplemented with Api137 Method: EM (single particle) / Resolution: 4.49 Å 51983 9ham EMDB-51983, PDB-9ham: C_(L29)-/(L22)- precursor supplemented with Api137 Method: EM (single particle) / Resolution: 5.06 Å
Source	escherichia coli (E. coli) apis mellifera (honey bee)
Keywords	RIBOSOME / antimicrobial peptide / RNA / ribosomal protein / PrAMP / proline-rich peptide / antibiotics / 50S / Api137