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	Saskemycin, a potent and selective antimycobacterial agent targeting a unique site on the ribosome.
Journal, issue, pages	Res Sq, Year 2025
Publish date	Nov 7, 2025
Authors	Gerard Wright / Michael Cook / Min Xu / Martino Morici / Dmitrii Travin / Wenliang Wang / Dorota Klepacki / Nandini Chhabra / Vishwas Rao / Henok Sahile / Dirk Hackenberger / Haaris Safdari / Max Berger / Martina Corazza / Austin Bond / Allison Guitor / Dominique Tertigas / Lijun Wang / Adam Schaenzer / Linda Ejim / Venkateswarlu Yarlagadda / James Gomez / Michael Surette / Yossef Av-Gay / Neeraj Dhar / Deborah Hung / Nora Vázquez-Laslop / Alexander Mankin / Daniel Wilson /
PubMed Abstract	Tuberculosis is the deadliest bacterial disease on the planet. The months-long regimen of multiple antibiotics required to treat tuberculosis profoundly affects the microbiome and leads to the ...Tuberculosis is the deadliest bacterial disease on the planet. The months-long regimen of multiple antibiotics required to treat tuberculosis profoundly affects the microbiome and leads to the development of antimicrobial resistance. Furthermore, non-tuberculous mycobacterial infections pose an increasing clinical challenge. Consequently, there is a growing need for new narrow-spectrum mycobacteria-targeting antibiotics with different mechanisms of action. Here, we report the discovery and characterization of a natural glycolipid antibiotic, saskemycin (SKM), which demonstrates potent and highly selective activity against mycobacteria. Genome sequencing, chemical analysis, and isotope feeding strategies reveal the unique structure and biosynthetic origin of SKM. SKM binds to the small ribosomal subunit at a site not targeted by any of the clinically relevant antibiotics acting on the ribosome. Bound to the ribosome, SKM corrupts the decoding center in a unique way, preventing stable binding of aminoacyl-tRNA in the A site and inhibiting translation in a sequence context-specific manner. Self-resistance in the producing organism is conferred by methylation of a single 16S rRNA nucleotide by SasO and SasN rRNA methyltransferases. These enzymes are orthologs of the ubiquitous RsmC and SpoU methyltransferases found in most bacterial genera but absent in mycobacteria, rationalizing SKM's exquisite selectivity. The discovery of SKM provides an entry point for the development of selective, microbiome-sparing antimycobacterial antibiotics with a unique structure, binding site, and mechanism of action.
External links	Res Sq / PubMed:41282059 / PubMed Central
Methods	EM (single particle)
Resolution	2.26 - 2.62 Å
Structure data	53311 9qqq EMDB-53311: Cryo-EM map of SKM-70S ribosomal stalled complex in the major state (vacant A-site, canon) PDB-9qqq: Cryo-EM structure of SKM-70S ribosomal stalled complex in the major state (vacant A-site, canon) Method: EM (single particle) / Resolution: 2.26 Å 53341 9qsj EMDB-53341, PDB-9qsj: Cryo-EM structure of SKM-70S ribosomal stalled complex in the A-tRNA positioned (Body open) state. Method: EM (single particle) / Resolution: 2.62 Å 55145 9sro EMDB-55145, PDB-9sro: Cryo-EM structure of SKM-70S ribosomal stalled complex in the rotated state with hybrid tRNAs Method: EM (single particle) / Resolution: 2.6 Å
Chemicals	ChemComp-ZN: Unknown entry PDB-1ja7: BINDING OF N-ACETYLGLUCOSAMINE TO CHICKEN EGG LYSOZYME: A POWDER DIFFRACTION STUDY ChemComp-MG: Unknown entry ChemComp-HOH: WATER PDB-1jai: H-RAS P21 PROTEIN MUTANT G12P, COMPLEXED WITH GUANOSINE-5'-[BETA,GAMMA-METHYLENE] TRIPHOSPHATE AND MANGANESE
Source	escherichia coli b (bacteria) streptococcus sanguinis (bacteria) escherichia coli (E. coli)
Keywords	RIBOSOME / Antibiotics / 70S complex / Body closure / Accomodation