9SS6

70S ribosome from RimM-KO

This is a non-PDB format compatible entry.

Summary for 9SS6

• Entry DOI: 10.2210/pdb9ss6/pdb
• EMDB information: 55178
• Descriptor: Small ribosomal subunit protein uS2, Small ribosomal subunit protein uS11, Small ribosomal subunit protein uS12, ... (54 entities in total)
• Functional Keywords: ribosome assembly, rimm, initiation factor if1, initiation factor if3, anti-association, ribosome
• Biological source: Escherichia coli; More
• Total number of polymer chains: 55
• Total formula weight: 2188483.72

Authors

Hassan, A.H.,Demo, G. (deposition date: 2025-09-25, release date: 2026-02-04)

Primary citation

Hassan, A.,Nakano, Y.,Gamper, H.,Masuda, I.,Pinkas, M.,Nagarajan, S.,Dworkin, J.,Blaha, G.,Hou, Y.M.,Demo, G.
Mechanistic insights into E. coli recovery from growth arrest.
Biorxiv, 2026

PubMed Abstract: Bacteria survive hostile conditions in clinically relevant conditions by shutting down protein synthesis, but how they restart growth remains poorly understood. Here, we use an Δ strain, which exhibits a prolonged growth arrest, as a model to investigate how bacteria recover from this arrested state and restore protein synthesis. RimM is a conserved ribosome maturation factor for the 3'-major (head) domain of the 16S rRNA within the bacterial 30S subunit. The loss of RimM causes a significantly longer delay in recovery than other 30S maturation factors, including RbfA - the presumed primary factor in 30S maturation. Cryo-EM analysis of Δ ribosomes revealed a delayed recruitment of ribosomal proteins to the 30S head domain and increased occupancy of the initiation factors IF1 and IF3, as well as recruitment of the silencing factor RsfS to the 50S subunit. These coordinated changes provide a safeguarding mechanism to block the assembly of premature 70S ribosomes. Notably, while the delayed 30S assembly in Δ reduces the activity of global protein synthesis during the recovery phase, bacteria attempt to compensate for this deficiency by producing higher levels of the ribosomal machinery, indicating a programmatic change in energy allocation to generate the ribosome machinery. These findings highlight the importance of the RimM-assisted assembly of the ribosomal head domain for bacterial recovery from growth arrest.

PubMed: 41542601
DOI: 10.64898/2026.01.09.698670

Experimental method

ELECTRON MICROSCOPY (2.6 Å)