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	A new family of bacterial ribosome hibernation factors.
Journal, issue, pages	Nature, Vol. 626, Issue 8001, Page 1125-1132, Year 2024
Publish date	Feb 14, 2024
Authors	Karla Helena-Bueno / Mariia Yu Rybak / Chinenye L Ekemezie / Rudi Sullivan / Charlotte R Brown / Charlotte Dingwall / Arnaud Baslé / Claudia Schneider / James P R Connolly / James N Blaza / Bálint Csörgő / Patrick J Moynihan / Matthieu G Gagnon / Chris H Hill / Sergey V Melnikov /
PubMed Abstract	To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage. In bacteria, two families of ...To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage. In bacteria, two families of hibernation factors have been described, but the low conservation of these proteins and the huge diversity of species, habitats and environmental stressors have confounded their discovery. Here, by combining cryogenic electron microscopy, genetics and biochemistry, we identify Balon, a new hibernation factor in the cold-adapted bacterium Psychrobacter urativorans. We show that Balon is a distant homologue of the archaeo-eukaryotic translation factor aeRF1 and is found in 20% of representative bacteria. During cold shock or stationary phase, Balon occupies the ribosomal A site in both vacant and actively translating ribosomes in complex with EF-Tu, highlighting an unexpected role for EF-Tu in the cellular stress response. Unlike typical A-site substrates, Balon binds to ribosomes in an mRNA-independent manner, initiating a new mode of ribosome hibernation that can commence while ribosomes are still engaged in protein synthesis. Our work suggests that Balon-EF-Tu-regulated ribosome hibernation is a ubiquitous bacterial stress-response mechanism, and we demonstrate that putative Balon homologues in Mycobacteria bind to ribosomes in a similar fashion. This finding calls for a revision of the current model of ribosome hibernation inferred from common model organisms and holds numerous implications for how we understand and study ribosome hibernation.
External links	Nature / PubMed:38355796 / PubMed Central
Methods	EM (single particle)
Resolution	2.6 - 3.1 Å
Structure data	19067 8rd8 EMDB-19067, PDB-8rd8: Cryo-EM structure of P. urativorans 70S ribosome in complex with hibernation factors Balon and RaiA (structure 1). Method: EM (single particle) / Resolution: 2.62 Å 19076 8rdv EMDB-19076, PDB-8rdv: Cryo-EM structure of P. urativorans 70S ribosome in complex with hibernation factor Balon, mRNA and P-site tRNA (structure 2). Method: EM (single particle) / Resolution: 2.6 Å 19077 8rdw EMDB-19077, PDB-8rdw: Cryo-EM structure of P. urativorans 70S ribosome in complex with hibernation factor Balon and EF-Tu(GDP) (structure 3). Method: EM (single particle) / Resolution: 2.74 Å 43074 8v9j EMDB-43074, PDB-8v9j: Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) (Structure 4) Method: EM (single particle) / Resolution: 3.1 Å 43075 8v9k EMDB-43075, PDB-8v9k: Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Rv2629 (Balon) (Structure 5) Method: EM (single particle) / Resolution: 3.1 Å 43076 8v9l EMDB-43076, PDB-8v9l: Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP) (Composite structure 6) Method: EM (single particle) / Resolution: 3.0 Å EMDB-43077: Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP) (Structure 6) Method: EM (single particle) / Resolution: 3.0 Å EMDB-43078: Hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP) bound to Mycobacterium smegmatis 70S ribosome, from focused 3D classification and refinement (Structure 6) Method: EM (single particle) / Resolution: 3.0 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-GDP: GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying moleculeYM / Guanosine diphosphate ChemComp-HOH: WATER / Water ChemComp-ZN*: Unknown entry
Source	psychrobacter urativorans (bacteria) mycolicibacterium smegmatis mc2 155 (bacteria) mycobacterium tuberculosis h37rv (bacteria)
Keywords	RIBOSOME / Hibernation factor / Dormancy / Balon / cryo-EM / mycobacteria / hibernation / Msmeg1130 / Rv2629 / MsmegEF-Tu