9ELY

raiA RNA motif (Clostridium acetobutylicum)

Summary for 9ELY

• Entry DOI: 10.2210/pdb9ely/pdb
• EMDB information: 48162
• Descriptor: raiA RNA (1 entity in total)
• Functional Keywords: raia, ncrna, rna
• Biological source: Clostridium acetobutylicum ATCC 824
• Total number of polymer chains: 1
• Total formula weight: 66465.44

Authors

Kretsch, R.C.,Wu, Y.,Nye, G.,Das, R.,Chiu, W. (deposition date: 2024-12-05, release date: 2025-04-23, Last modification date: 2025-07-30)

Primary citation

Kretsch, R.C.,Wu, Y.,Shabalina, S.A.,Lee, H.,Nye, G.,Koonin, E.V.,Gao, A.,Chiu, W.,Das, R.
Naturally ornate RNA-only complexes revealed by cryo-EM.
Nature, 643:1135-1142, 2025

PubMed Abstract: 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.

PubMed: 40328315
DOI: 10.1038/s41586-025-09073-0

Experimental method

ELECTRON MICROSCOPY (2.9 Å)