9ZCA | pdb_00009zca

5-methyl-cytidine twist corrected RNA origami 6-helix bundle type-2 dimer

• PDB DOI: https://doi.org/10.2210/pdb9ZCA/pdb
• EM Map EMD-74032: EMDB EMDataResource
• NAKB: 9ZCA

• Classification: RNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2025-11-22 Released: 2025-12-10 
• Deposition Author(s): McRae, E.K.S., Yadav, D.K.
• Funding Organization(s): Cancer Prevention and Research Institute of Texas (CPRIT)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 11.5 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.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 475.7 kDa 
• Atom Count: 31,479 
• Modeled Residue Count: 1,460 
• Deposited Residue Count: 1,460 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5-methyl-cytidine twist corrected RNA origami 6-helix bundle	A, B	730	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 11.5 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-10 
Deposition Author(s): McRae, E.K.S., Yadav, D.K.

---

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

Revision History  

• Version 1.0: 2025-12-10
  Type: Initial release