9ZC6 | pdb_00009zc6

5-methyl-cytidine L-21 ScaI Tetrahymena Ribozyme

• PDB DOI: https://doi.org/10.2210/pdb9ZC6/pdb
• EM Map EMD-70041: EMDB EMDataResource
• NAKB: 9ZC6

• Classification: RNA
• Organism(s): Tetrahymena thermophila
• Mutation(s): No 


• Deposited: 2025-11-22 Released: 2025-12-03 
• Deposition Author(s): McRae, E.K.S.
• Funding Organization(s): Cancer Prevention and Research Institute of Texas (CPRIT)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Base modifications reshape RNA folding landscapes and structure function relationships in synthetic and natural RNAs

Kumar, D.Y., Yang, H., Lee, S., McRae, E.K.S.

To be published.

Biological Assembly 1  

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 126.4 kDa 
• Atom Count: 8,354 
• Modeled Residue Count: 387 
• Deposited Residue Count: 388 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5-methyl-cytidine L-21 ScaI Tetrahymena Ribozyme	A	388	Tetrahymena thermophila

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.6.2
MODEL REFINEMENT	ISOLDE
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): McRae, E.K.S.

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Funding Organization	Location	Grant Number
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RR230015

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release