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.

(2026) RSC Chem Biol 

• PubMed: 42100640 
• DOI: https://doi.org/10.1039/d6cb00055j
• Primary Citation Related Structures: 
  23JY, 23JZ, 23KA


• PubMed Abstract: 
  

  Amiloride possesses a characteristic chemical scaffold capable of recognizing uracil (U) through three complementary hydrogen bonds; however, its binding selectivity toward naturally occurring RNA structural motifs has remained uncharacterized. In this study, we present a large-scale analysis of amiloride's RNA binding properties and structural characterization of the amiloride-RNA complex. Using folded RNA element profiling with structure library (FOREST), we evaluated the RNA-binding selectivity of amiloride across 3000 structured RNA motifs and uncovered pronounced binding preferences for G-quadruplexes and, notably, for a specific internal loop motif containing a U-U mismatch ( K _Dapp = 0.31 µM). Furthermore, a motif extraction strategy was used to enable detailed structural investigation. The X-ray crystal structure of the amiloride-RNA complex provides the first structural evidence that amiloride recognizes a U residue within a naturally occurring RNA context via its signature complementary hydrogen bonding interactions.

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Organizational Affiliation: 
• Institute of Multidisciplinary Research for Advanced Materials, Tohoku University Miyagi 980-8577 Japan [e-mail] [e-mail].
Department of Chemistry, Graduate School of Science, Tohoku University Miyagi 980-8578 Japan.
Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University Miyagi 980-8577 Japan.
Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University Tokyo 102-8554 Japan [e-mail].
Center for iPS Cell Research and Application (CiRA), Kyoto University Kyoto 606-8507 Japan.
Institute for Quantitative Biosciences, The University of Tokyo Tokyo 113-0032 Japan.

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
  
• Version 1.1: 2026-05-20
  Changes: Database references