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TitleStructure of an archaeal ribosome reveals a divergent active site and hibernation factor.
Journal, issue, pagesNat Microbiol, Vol. 10, Issue 8, Page 1940-1953, Year 2025
Publish dateJul 17, 2025
AuthorsAmos J Nissley / Yekaterina Shulgina / Roan W Kivimae / Blake E Downing / Petar I Penev / Jillian F Banfield / Dipti D Nayak / Jamie H D Cate /
PubMed AbstractRibosomes translate mRNA into protein. Despite divergence in ribosome structure over the course of evolution, the catalytic site, known as the peptidyl transferase centre (PTC), is thought to be ...Ribosomes translate mRNA into protein. Despite divergence in ribosome structure over the course of evolution, the catalytic site, known as the peptidyl transferase centre (PTC), is thought to be nearly universally conserved. Here we identify clades of archaea that have highly divergent ribosomal RNA sequences in the PTC. To understand how these PTC sequences fold, we determined cryo-EM structures of the 70S and 50S ribosomes to 2.4 Å and 2 Å, respectively, from the hyperthermophilic archaeon Pyrobaculum calidifontis. PTC sequence variation leads to the rearrangement of key base triples, and differences between archaeal and bacterial ribosomal proteins enable sequence variation in archaeal PTCs. Finally, we identify an archaeal ribosome hibernation factor, Dri, that differs from known bacterial and eukaryotic hibernation factors and is found in multiple archaeal phyla. Overall, this work identifies factors that regulate ribosome function in archaea and reveals a larger diversity of the most ancient sequences in the ribosome.
External linksNat Microbiol / PubMed:40676158
MethodsEM (single particle)
Resolution1.95 - 2.79 Å
Structure data

47578

9e6q

EMDB-47578, PDB-9e6q:
Cryo-EM structure of the Pyrobaculum calidifontis 50S ribosomal subunit in complex with Dri
Method: EM (single particle) / Resolution: 1.95 Å

EMDB-47604: Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome (Consensus Map)
Method: EM (single particle) / Resolution: 2.36 Å

EMDB-47605: Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome (50S focused refinement)
Method: EM (single particle) / Resolution: 2.22 Å

EMDB-47606: Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome (CP focused refinement)
Method: EM (single particle) / Resolution: 2.42 Å

EMDB-47611: Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome (30S focused refinement)
Method: EM (single particle) / Resolution: 2.51 Å

EMDB-47617: Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome (30S head focused refinement)
Method: EM (single particle) / Resolution: 2.71 Å

47628

9e71

EMDB-47628: Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome (Composite Map)
PDB-9e71: Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome
Method: EM (single particle) / Resolution: 2.36 Å

EMDB-47662: Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome in complex with Dri (Consensus Map)
Method: EM (single particle) / Resolution: 2.53 Å

EMDB-47664: Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome in complex with Dri (50S focused refinement)
Method: EM (single particle) / Resolution: 2.37 Å

EMDB-47666: Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome in complex with Dri (30S focused refinement)
Method: EM (single particle) / Resolution: 2.67 Å

EMDB-47667: Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome in complex with Dri (30S head focused refinement)
Method: EM (single particle) / Resolution: 2.79 Å

47668

9e7f

EMDB-47668: Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome in complex with Dri (Composite Map)
PDB-9e7f: Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome in complex with Dri
Method: EM (single particle) / Resolution: 2.53 Å

Chemicals

ChemComp-SPM:
SPERMINE

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER

Source
  • pyrobaculum calidifontis jcm 11548 (archaea)
KeywordsRIBOSOME / Translation / Hibernation / RNA

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