9G7C | pdb_00009g7c

Cryo-EM structure of raiA ncRNA from Clostridium reveals a new RNA 3D fold

• PDB DOI: https://doi.org/10.2210/pdb9G7C/pdb
• NAKB: 9G7C
• EM Map EMD-51119: EMDB EMDataResource

• Classification: RNA
• Organism(s): Clostridium sp. CAG:138
• Mutation(s): No 


• Deposited: 2024-07-20 Released: 2024-10-30 
• Deposition Author(s): Badepally, N.G., Moura, T.R., Purta, E., Baulin, E., Bujnicki, J.M.
• Funding Organization(s): Polish National Science Centre

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.27 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM Structure of raiA ncRNA From Clostridium Reveals a New RNA 3D Fold.

Badepally, N.G., de Moura, T.R., Purta, E., Baulin, E.F., Bujnicki, J.M.

(2024) J Mol Biology 436: 168833-168833

• PubMed: 39454748 
• DOI: https://doi.org/10.1016/j.jmb.2024.168833
• Primary Citation Related Structures: 
  9G7C


• PubMed Abstract: 
  

  Advancements in genome-wide sequence analysis have led to the discovery of numerous novel bacterial non-coding RNAs (ncRNAs). These ncRNAs have been categorized into various RNA families and classes based on their size, structure, function, and evolutionary relationships. One such ncRNA family, raiA, is notably abundant in the bacterial phyla Firmicutes and Actinobacteria and is remarkably well-conserved across many Gram-positive bacteria. In this study, we integrated cryo-electron microscopy single-particle analysis with computational modeling and biochemical techniques to elucidate the structural characteristics of raiA from Clostridium sp. CAG 138. Our findings reveal the globular 3D fold of raiA, providing valuable structural insights. This analysis paves the way for future investigations into the functional properties of raiA, potentially uncovering new regulatory mechanisms in bacterial ncRNAs.

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Organizational Affiliation: 
• Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland.
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland. Electronic address: [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 72.83 kDa 
• Atom Count: 4,826 
• Modeled Residue Count: 224 
• Deposited Residue Count: 224 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
raiA (224-MER)	A	224	Clostridium sp. CAG:138

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.27 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-10-30 
Deposition Author(s): Badepally, N.G., Moura, T.R., Purta, E., Baulin, E., Bujnicki, J.M.

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Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	--

Revision History  

• Version 1.0: 2024-10-30
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references