9FDA
Structure of E. coli 30S-IF1-IF3-mRNA-Edeine complex
Summary for 9FDA
| Entry DOI | 10.2210/pdb9fda/pdb |
| EMDB information | 50327 |
| Descriptor | Small ribosomal subunit protein uS4, Small ribosomal subunit protein bS16, Small ribosomal subunit protein uS17, ... (19 entities in total) |
| Functional Keywords | ribosomes, 30s subunit, antibiotic, 30s inhibitors, translation |
| Biological source | Escherichia coli More |
| Total number of polymer chains | 15 |
| Total formula weight | 688057.86 |
| Authors | |
| Primary citation | Safdari, H.A.,Morici, M.,Sanchez-Castro, A.,Dallape, A.,Paternoga, H.,Giuliodori, A.M.,Fabbretti, A.,Milon, P.,Wilson, D.N. The translation inhibitors kasugamycin, edeine and GE81112 target distinct steps during 30S initiation complex formation. Nat Commun, 16:2470-2470, 2025 Cited by PubMed Abstract: During bacterial translation initiation, the 30S ribosomal subunit, initiation factors, and initiator tRNA define the reading frame of the mRNA. This process is inhibited by kasugamycin, edeine and GE81112, however, their mechanisms of action have not been fully elucidated. Here we present cryo-electron microscopy structures of 30S initiation intermediate complexes formed in the presence of kasugamycin, edeine and GE81112 at resolutions of 2.0-2.9 Å. The structures reveal that all three antibiotics bind within the E-site of the 30S and preclude 30S initiation complex formation. While kasugamycin and edeine affect early steps of 30S pre-initiation complex formation, GE81112 stalls pre-initiation complex formation at a further step by allowing start codon recognition, but impeding IF3 departure. Collectively, our work highlights how chemically distinct compounds binding at a conserved site on the 30S can interfere with translation initiation in a unique manner. PubMed: 40075065DOI: 10.1038/s41467-025-57731-8 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2 Å) |
Structure validation
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