9NTA
Methanosarcina acetivorans 50S subunit obtained from methanol-grown cells
This is a non-PDB format compatible entry.
Summary for 9NTA
| Entry DOI | 10.2210/pdb9nta/pdb |
| EMDB information | 49757 |
| Descriptor | 23S rRNA, Large ribosomal subunit protein uL13, Large ribosomal subunit protein uL14, ... (35 entities in total) |
| Functional Keywords | archaea, methanosarcina acetivorans, large subunit, 50s subunit, growth conditions, methanol, ribosome |
| Biological source | Methanosarcina acetivorans More |
| Total number of polymer chains | 32 |
| Total formula weight | 1427873.26 |
| Authors | Ghosh, A.,Fordjour, G.N.R.,Armache, J.-P.,Ferry, J.G.,Murakami, K.S.,Bevilacqua, P.C. (deposition date: 2025-03-18, release date: 2025-09-24, Last modification date: 2025-11-05) |
| Primary citation | Fordjour, G.N.R.,Ghosh, A.,Ferry, J.G.,Armache, J.P.,Bevilacqua, P.C.,Murakami, K.S. Cryo-EM study and in vivo chemical mapping of the Methanosarcina acetivorans ribosome and its dimerization via a repurposed enzyme and translation factor. J.Biol.Chem., 301:110686-110686, 2025 Cited by PubMed Abstract: Despite the overall conservation of ribosomes across all domains of life, differences in their 3D architecture, rRNA sequences, ribosomal protein composition, and translation factor requirements reflect lineage-specific adaptations to environmental niches. In the domain Archaea, structural studies have primarily focused on non-methanogenic thermophiles and halophiles, leaving it unclear whether these represent the broader archaeal domain. Here, we report the cryo-electron microscopy (cryo-EM) structure of the ribosome from Methanosarcina acetivorans, a previously unreported high-resolution structure from a model mesophilic methanogenic archaeon. Compared to ribosomes from extremophiles, the M. acetivorans ribosome has a simplified architecture, lacking paralogous duplications and containing a reduced complement of ribosomal proteins. Structures of the large subunit (50S) from cells grown with either methanol or acetate show conserved rRNA folding and protein composition. High-resolution structures of the 50S subunit from the two growth substrates enabled us to investigate structural properties that may influence in vivo dimethyl sulfate (DMS) reactivity, an orthogonal chemical approach used to probe RNA structure. We observed good agreement between in vivo DMS reactivity and ribosome structure. Finally, we identify a previously uncharacterized ribosome dimerization mode involving only 50S subunits and mediated by a heterotetrameric complex of PurH and aEF2-proteins with alternative metabolic and translational roles. This macromolecular assembly, which we term the Methanogen Ribosome Dimerization Factor (MRDF), likely mediates ribosome hibernation, revealing an alternative regulatory mechanism in translation. PubMed: 40914243DOI: 10.1016/j.jbc.2025.110686 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.38 Å) |
Structure validation
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