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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 AbstractThe structures of natural RNAs remain poorly characterized and may hold numerous surprises. Here we report three-dimensional structures of three large ornate bacterial RNAs using cryo-electron ...The structures of natural RNAs remain poorly characterized and may hold numerous surprises. Here we report three-dimensional structures of three large ornate bacterial RNAs using cryo-electron microscopy (cryo-EM). GOLLD (Giant, Ornate, Lake- and Lactobacillales-Derived), ROOL (Rumen-Originating, Ornate, Large) and OLE (Ornate Large Extremophilic) RNAs form homo-oligomeric complexes whose stoichiometries are retained at lower concentrations than measured in cells. 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, each empty except for a disordered loop. Extensive intramolecular 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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