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Naturally ornate RNA-only complexes revealed by cryo-EM

Author

Listed:
  • Rachael C. Kretsch

    (Stanford University)

  • Yuan Wu

    (Stanford University)

  • Svetlana A. Shabalina

    (National Institutes of Health)

  • Hyunbin Lee

    (Stanford University School of Medicine)

  • Grace Nye

    (SSRL–SLAC National Accelerator Laboratory)

  • Eugene V. Koonin

    (National Institutes of Health)

  • Alex Gao

    (Stanford University
    Stanford University School of Medicine)

  • Wah Chiu

    (Stanford University
    SSRL–SLAC National Accelerator Laboratory
    Stanford University
    Stanford University)

  • Rhiju Das

    (Stanford University
    Stanford University
    Stanford University School of Medicine)

Abstract

The structures of natural RNAs remain poorly characterized and may hold numerous surprises1–4. 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.

Suggested Citation

  • Rachael C. Kretsch & Yuan Wu & Svetlana A. Shabalina & Hyunbin Lee & Grace Nye & Eugene V. Koonin & Alex Gao & Wah Chiu & Rhiju Das, 2025. "Naturally ornate RNA-only complexes revealed by cryo-EM," Nature, Nature, vol. 643(8073), pages 1135-1142, July.
    • Handle: RePEc:nat:nature:v:643:y:2025:i:8073:d:10.1038_s41586-025-09073-0
    DOI: 10.1038/s41586-025-09073-0
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