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DOE OSTI · 2575396

Naturally ornate RNA-only complexes revealed by cryo-EM

Kretsch, Rachael C. [Stanford Univ., CA (United States)] (ORCID:000000026935518X)·Wu, Yuan [Stanford Univ., CA (United States)]·Shabalina, Svetlana A. [National Institutes of Health (NIH), Bethesda, MD (United States)] (ORCID:000000023774819X)·Lee, Hyunbin [Stanford Univ., CA (United States). School of Medicine] (ORCID:000900061911435X)·Nye, Grace [SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)]·Koonin, Eugene V. [National Institutes of Health (NIH), Bethesda, MD (United States)] (ORCID:0000000339438299)·Gao, Alex [Stanford Univ., CA (United States). School of Medicine] (ORCID:0000000235790327)·Chiu, Wah [Stanford Univ., CA (United States); SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)] (ORCID:0000000289103078)·Das, Rhiju [Stanford Univ., CA (United States). School of Medicine] (ORCID:0000000174970972)
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Abstract

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.

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59 BASIC BIOLOGICAL SCIENCESComputational biophysicsCryoelectron microscopyMolecular biophysics

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Kretsch, Rachael C. [Stanford Univ., CA (United States)] (ORCID:000000026935518X), Wu, Yuan [Stanford Univ., CA (United States)], Shabalina, Svetlana A. [National Institutes of Health (NIH), Bethesda, MD (United States)] (ORCID:000000023774819X), Lee, Hyunbin [Stanford Univ., CA (United States). School of Medicine] (ORCID:000900061911435X), Nye, Grace [SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)], Koonin, Eugene V. [National Institutes of Health (NIH), Bethesda, MD (United States)] (ORCID:0000000339438299), Gao, Alex [Stanford Univ., CA (United States). School of Medicine] (ORCID:0000000235790327), Chiu, Wah [Stanford Univ., CA (United States); SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)] (ORCID:0000000289103078), Das, Rhiju [Stanford Univ., CA (United States). School of Medicine] (ORCID:0000000174970972). 2025-05-06. Naturally ornate RNA-only complexes revealed by cryo-EM. https://doi.org/10.1038/s41586-025-09073-0

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