9SRD
Cryo-EM structure of P. abyssi 70S ribosome in complex with hibernation factor HibA (HibA-uL5 conformation)
This is a non-PDB format compatible entry.
Summary for 9SRD
| Entry DOI | 10.2210/pdb9srd/pdb |
| EMDB information | 55138 |
| Descriptor | rRNA 23S, 30S ribosomal protein S6e, 30S ribosomal protein S7, ... (67 entities in total) |
| Functional Keywords | 70s, ribosome, hibernation, pyrococcus abyssi |
| Biological source | Pyrococcus abyssi GE5 More |
| Total number of polymer chains | 69 |
| Total formula weight | 2541080.83 |
| Authors | Madru, C.,Bourgeois, G.,Mechulam, Y.,Schmitt, E. (deposition date: 2025-09-24, release date: 2026-05-13) |
| Primary citation | Madru, C.,Bourgeois, G.,Dulermo, R.,Capeyrou, R.,Joncour, G.,Figuigui, K.,Duchateau, M.,Chamot-Rooke, J.,Duboc, C.,l'Haridon, S.,Mc Teer, L.,Kwapisz, M.,Clouet-d'Orval, B.,Bouvier, M.,Mechulam, Y.,Borrel, G.,Schmitt, E.,Flament, D. A family of ribosome hibernation factors widespread in Archaea. Nat Commun, 2026 Cited by PubMed Abstract: Ribosome hibernation preserves translation machinery during stress, yet its mechanisms in Archaea remain poorly defined. Using cryo-EM analysis, we studied hibernation pathways in Pyrococcus abyssi stressed cells. We identified HibA, a previously unrecognized family of hibernation factors widespread in Archaea. HibA consists of a bacterial-like HPF/RaiA domain fused to a Cystathionine Beta Synthase module. Unexpectedly, HibA binds to the ribosome in three different conformations, occupying the A, P and E sites of tRNAs, as well as that of mRNA, enhancing its ability to protect the ribosome from degradation. Idle ribosomes also frequently accumulate the archaeal homolog of eukaryotic ribosome maturation protein SBDS (aSBDS), suggesting that stressed archaeal cells may engage parallel hibernation routes in which aSBDS can complement HibA. Deletion of hibA in Thermococcus barophilus delays recovery from stationary phase and reduces 70S ribosome pools, establishing its role in ribosome preservation. Taxonomic profiling shows that many archaeal lineages encode distinct repertoires of ribosome-associated protection factors, underscoring the modular and multi-layered nature of archaeal hibernation systems. In addition, a comprehensive phylogenetic analysis highlights the evolutionary relationships between prevalent ribosome hibernation factors across Bacteria and Archaea. PubMed: 42045235DOI: 10.1038/s41467-026-72341-8 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.1 Å) |
Structure validation
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