9ELY | pdb_00009ely

raiA RNA motif (Clostridium acetobutylicum)

• PDB DOI: https://doi.org/10.2210/pdb9ELY/pdb
• NAKB: 9ELY
• EM Map EMD-48162: EMDB EMDataResource

• Classification: RNA
• Organism(s): Clostridium acetobutylicum ATCC 824
• Mutation(s): No 


• Deposited: 2024-12-05 Released: 2025-04-23 
• Deposition Author(s): Kretsch, R.C., Wu, Y., Nye, G., Das, R., Chiu, W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Naturally ornate RNA-only complexes revealed by cryo-EM.

Kretsch, R.C., Wu, Y., Shabalina, S.A., Lee, H., Nye, G., Koonin, E.V., Gao, A., Chiu, W., Das, R.

(2025) Nature 643: 1135-1142

• PubMed: 40328315 
• DOI: https://doi.org/10.1038/s41586-025-09073-0
• Primary Citation of Related Structures:  
  9ELY, 9MCW, 9MDS, 9MEE


• PubMed Abstract: 
  

  Myriad families of natural RNAs have been proposed, but not yet experimentally shown, to form biologically important structures ^1-4 . 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.

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Organizational Affiliation: 
• Biophysics Program, Stanford University, Stanford, CA, USA.
Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
Computational Biology Branch, Division of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
Biophysics Program, Stanford University, Stanford, CA, USA. [e-mail].
Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA. [e-mail].
Department of Bioengineering and James Clark Center, Stanford University, Stanford, CA, USA. [e-mail].
Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA. [e-mail].
Biophysics Program, Stanford University, Stanford, CA, USA. [e-mail].
Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA. [e-mail].
Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 66.47 kDa 
• Atom Count: 4,334 
• Modeled Residue Count: 202 
• Deposited Residue Count: 205 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
raiA RNA	A	205	Clostridium acetobutylicum ATCC 824

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.5.3
MODEL REFINEMENT	PHENIX	1.21
MODEL REFINEMENT	Rosetta	3.10
MODEL REFINEMENT	ISOLDE	1,8
MODEL REFINEMENT	Coot	0.9.8

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-23 
Deposition Author(s): Kretsch, R.C., Wu, Y., Nye, G., Das, R., Chiu, W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM122579
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U24 GM129541
National Science Foundation (NSF, United States)	United States	2330652

Revision History  

• Version 1.0: 2025-04-23
  Type: Initial release
  
• Version 1.1: 2025-05-21
  Changes: Data collection, Database references
• Version 1.2: 2025-07-30
  Changes: Data collection, Database references