9ZBR | pdb_00009zbr

1-methyl-pseudouridine L-21 ScaI Tetrahymena Ribozyme - extended conformation

• PDB DOI: https://doi.org/10.2210/pdb9ZBR/pdb
• EM Map EMD-73998: EMDB EMDataResource
• NAKB: 9ZBR

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


• Deposited: 2025-11-21 Released: 2025-12-03 
• Deposition Author(s): McRae, E.K.S., Yang, H.
• Funding Organization(s): Cancer Prevention and Research Institute of Texas (CPRIT)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 7.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Base modifications shift tertiary structure and activity in synthetic RNA origami and a natural ribozyme.

Yadav, D.K., Yang, H., Lee, S., McRae, E.K.S.

(2026) Nat Commun 

• PubMed: 42128887 
• DOI: https://doi.org/10.1038/s41467-026-72891-x
• Primary Citation Related Structures: 
  9ZBQ, 9ZBR, 9ZC6, 9ZC7, 9ZC8, 9ZC9, 9ZCA, 9ZCB, 9ZCC


• PubMed Abstract: 
  

  Modified nucleotide bases like 5-methylcytosine (m5C) and N1-methyl-pseudouridine (m1Ψ) are widely used to enhance stability and reduce immunogenicity in therapeutic RNAs, yet their impact on RNA tertiary structure remains unclear. Here we investigate how these modifications influence folding and function in both a synthetic RNA origami nanostructure and the natural Tetrahymena ribozyme. Using cryo-EM, FRET, and biochemical assays, we find that modified bases impede proper maturation of RNA origami by stabilizing alternative coaxial stacking at key junctions, leading to dimerization. In the ribozyme, modifications shift the equilibrium between open and closed conformations, altering catalytic activity in a temperature-dependent manner. These effects arise primarily from changes in base-stacking energetics rather than base pairing. Our findings reveal that base modifications reshape RNA folding landscapes and structure-function relationships, underscoring the need to consider structural consequences when designing modified RNAs for synthetic biology and therapeutic applications.

---

Organizational Affiliation: 
• Houston Methodist Research Institute (HMRI), Houston, TX, USA.
Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.
Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX, USA.
Houston Methodist Research Institute (HMRI), Houston, TX, USA. [e-mail].
Department of Biochemistry in Medicine, Weill Cornell Medical College, Cornell University, New York, NY, USA. [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 126.46 kDa 
• Atom Count: 8,380 
• Modeled Residue Count: 387 
• Deposited Residue Count: 387 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
1-methyl-pseudouridine L-21 ScaI Tetrahymena Ribozyme	A	387	Tetrahymena thermophila

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 7.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

---

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
  
• Version 1.1: 2026-06-17
  Changes: Data collection, Database references