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TitleNaturally ornate RNA-only complexes revealed by cryo-EM.
Journal, issue, pagesNature, Year 2025
Publish dateMay 6, 2025
AuthorsRachael C Kretsch / Yuan Wu / Svetlana A Shabalina / Hyunbin Lee / Grace Nye / Eugene V Koonin / Alex Gao / Wah Chiu / Rhiju Das /
PubMed AbstractMyriad families of natural RNAs have been proposed, but not yet experimentally shown, to form biologically important structures. Here we report three-dimensional structures of three large ornate ...Myriad families of natural RNAs have been proposed, but not yet experimentally shown, to form biologically important structures. Here we report three-dimensional structures of three large ornate bacterial RNAs using cryogenic electron microscopy at resolutions of 2.9-3.1 Å. Without precedent among previously characterized natural RNA molecules, Giant, Ornate, Lake- and Lactobacillales-Derived (GOLLD), Rumen-Originating, Ornate, Large (ROOL), and Ornate Large Extremophilic (OLE) RNAs form homo-oligomeric complexes whose stoichiometries are retained at concentrations lower than expected in the cell. OLE RNA forms a dimeric complex with long co-axial pipes spanning two monomers. Both GOLLD and ROOL form distinct RNA-only multimeric nanocages with diameters larger than the ribosome, empty except for a disordered loop. Extensive intra- and intermolecular A-minor interactions, kissing loops, an unusual A-A helix, and other interactions stabilize the three complexes. Sequence covariation analysis of these large RNAs reveals evolutionary conservation of intermolecular interactions, supporting the biological importance of large, ornate RNA quaternary structures that can assemble without any involvement of proteins.
External linksNature / PubMed:40328315
MethodsEM (single particle)
Resolution2.9 - 3.7 Å
Structure data

48162

9ely

EMDB-48162, PDB-9ely:
raiA RNA motif (Clostridium acetobutylicum)
Method: EM (single particle) / Resolution: 2.9 Å

48163

9mcw

EMDB-48163, PDB-9mcw:
OLE RNA dimer (Clostridium acetobutylicum)
Method: EM (single particle) / Resolution: 2.9 Å

48179

9mds

EMDB-48179, PDB-9mds:
ROOL RNA nanocage (env-120)
Method: EM (single particle) / Resolution: 3.1 Å

48214

9mee

EMDB-48214, PDB-9mee:
GOLLD RNA nanocage (env-38)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-70247: Focused refinement of ' domain of a subunit of GOLLD RNA nanocage.
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-70248: Focused refinement of 5' domain of a single subunit of GOLLD RNA nanocage.
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-70249: D7 reconstruction of GOLLD nanocage
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-70250: Focused refinement of one subunit or ROOL RNA nanocage
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-70251: D4 reconstruction of ROOL RNA nanocage
Method: EM (single particle) / Resolution: 3.5 Å

Source
  • clostridium acetobutylicum atcc 824 (bacteria)
  • synthetic construct (others)
KeywordsRNA / raiA / ncRNA / OLE / ROOL / nanocage / GOLLD

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