23JY | pdb_000023jy

pre-miR-6074 internal loop

• PDB DOI: https://doi.org/10.2210/pdb23JY/pdb
• NAKB: 23JY

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


• Deposited: 2026-02-09 Released: 2026-05-06 
• Deposition Author(s): Kondo, J., Okada, M., Tsuzuki, K., Onizuka, K., Nagasawa, R., Miyashita, E., Komatsu, K.R., Saito, H., Nagatsugi, F.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.245 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

RNA-binding Landscape of Amiloride: Large-scale Profiling and Structural Basis of U-U Mismatch Recognition

Tsuzuki, K., Onizuka, K., Okada, M., Nagasawa, R., Miyashita, E., Komatsu, K.R., Saito, H., Kondo, J., Nagatsugi, F.

(2025) RSC Chem Biol 

• DOI: https://doi.org/10.1039/D6CB00055J

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 14.08 kDa 
• Atom Count: 863 
• Modeled Residue Count: 40 
• Deposited Residue Count: 44 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*UP*GP*CP*GP*GP*AP*UP*AP*CP*CP*CP*GP*GP*GP*UP*UP*GP*CP*CP*GP*C)-3')	A, B	22	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.245 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.662	α = 90
b = 66.662	β = 90
c = 53.348	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-06 
Deposition Author(s): Kondo, J., Okada, M., Tsuzuki, K., Onizuka, K., Nagasawa, R., Miyashita, E., Komatsu, K.R., Saito, H., Nagatsugi, F.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP25ama121014

Revision History  

• Version 1.0: 2026-05-06
  Type: Initial release