9T1A

E. coli 70S ribosome from delta-RlmE strain, PTC class 1

Summary for 9T1A

• Entry DOI: 10.2210/pdb9t1a/pdb
• EMDB information: 55428
• Descriptor: tRNA(Phe), Large ribosomal subunit protein uL16, Large ribosomal subunit protein bL21, ... (18 entities in total)
• Functional Keywords: rna modifications, ribosome biogenesis, maturation, ribosome
• Biological source: Escherichia coli; More
• Total number of polymer chains: 14
• Total formula weight: 1194937.47

Authors

Larsson, D.S.D.,Selmer, M. (deposition date: 2025-10-21, release date: 2026-03-18, Last modification date: 2026-08-26)

Primary citation

Larsson, D.S.D.,Liiv, A.,Ero, R.,Remme, J.,Selmer, M.
23S rRNA modifications stimulate catalytic activity and prevent the formation of alternative structures.
Nucleic Acids Res., 54:-, 2026

PubMed Abstract: Ribosomal RNA (rRNA) modifications cluster around the peptidyl transferase centre (PTC), the catalytic centre of the ribosome, yet their collective functional roles remain unclear. Here we analyse Escherichia coli ribosomes lacking 11 or 12 modifications near the PTC. Using kinetic assays, we show these hypo-modified ribosomes catalyse peptide bond formation at rates twofold to threefold lower than wild-type and exhibit reduced thermal stability. Cryo-electron microscopy of hypo-modified ribosomes reveals multiple alternative conformations of the PTC and exit tunnel regions, disrupting native stacking and hydrogen bonding critical for positioning of transfer RNA substrates. These findings indicate that rRNA modifications stabilize the native PTC structure, preventing formation of alternative, nonfunctional conformations and thereby enhancing catalytic efficiency. Our study provides insight into how rRNA modifications fine-tune ribosome function by maintaining structural integrity essential for efficient translation.

PubMed: 42598854
DOI: 10.1093/nar/gkag800

Experimental method

ELECTRON MICROSCOPY (2.39 Å)