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	Mechanistic insights into recovery from growth arrest.
Journal, issue, pages	bioRxiv, Year 2026
Publish date	Jan 9, 2026
Authors	Ahmed Hassan / Yuko Nakano / Howard Gamper / Isao Masuda / Matyas Pinkas / Sathya Nagarajan / Jonathan Dworkin / Gregor Blaha / Ya-Ming Hou / Gabriel Demo /
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 ...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.
External links	bioRxiv / PubMed:41542601 / PubMed Central
Methods	EM (single particle)
Resolution	2.6 - 3.1 Å
Structure data	55171 9ss0 EMDB-55171, PDB-9ss0: 30S ribosomal subunit RimM-KO with IF1 and IF3 (State I) Method: EM (single particle) / Resolution: 3.0 Å 55173 9ss1 EMDB-55173, PDB-9ss1: 30S ribosomal subunit RimM-KO with IF1 and IF3 (State II) Method: EM (single particle) / Resolution: 2.9 Å 55174 9ss2 EMDB-55174, PDB-9ss2: 30S ribosomal subunit RimM-KO with IF1 and IF3 (State III) Method: EM (single particle) / Resolution: 2.9 Å 55176 9ss4 EMDB-55176, PDB-9ss4: pre-50S ribosomal subunit in rimM-KO with RsfS (-H68) Method: EM (single particle) / Resolution: 2.7 Å 55177 9ss5 EMDB-55177, PDB-9ss5: 50S ribosomal subunit in rimM-KO with RsfS (+H68) Method: EM (single particle) / Resolution: 2.7 Å 55178 9ss6 EMDB-55178, PDB-9ss6: 70S ribosome from RimM-KO Method: EM (single particle) / Resolution: 2.6 Å EMDB-55181: 30S ribosomal subunit RimM-WT with IF1 and IF3 Method: EM (single particle) / Resolution: 3.1 Å EMDB-55182: pre-50S ribosomal subunit from RimM-WT with RsfS (-H68) Method: EM (single particle) / Resolution: 2.7 Å EMDB-55183: 50S ribosomal subunit from RimM-WT with RsfS (+H68) Method: EM (single particle) / Resolution: 2.7 Å EMDB-55185: 70S ribosome from RimM-WT Method: EM (single particle) / Resolution: 3.0 Å
Source	escherichia coli (E. coli)
Keywords	RIBOSOME / Ribosome assembly / RimM / initiation factor IF1 / initiation factor IF3 / anti-association