7F8Z | pdb_00007f8z

RNA kink-turn motif with 2-aminopurine

• PDB DOI: https://doi.org/10.2210/pdb7F8Z/pdb
• NAKB: 7F8Z

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


• Deposited: 2021-07-03 Released: 2022-07-06 
• Deposition Author(s): Kondo, J., Miyauchi, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Structure-based design of a sequence-specific RNA probe that mimics the kink-turn motif

Miyauchi, T., Yamaguchi, K., Saisu, S., Kondo, J.

(2025) Nar Mol Med 2

• DOI: https://doi.org/10.1093/narmme/ugaf006

Biological Assembly 1  

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

Biological Assembly 2  

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

Biological assembly 5 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.37 kDa 
• Atom Count: 4,146 
• Modeled Residue Count: 190 
• Deposited Residue Count: 190 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(2PR))-R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')	A, B, C, D, E, F, G, H, I, J	19	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	K [auth A], L [auth C], M [auth F], N [auth G], O [auth J]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.962	α = 90
b = 87.726	β = 90
c = 124.273	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-07-06 
Deposition Author(s): Kondo, J., Miyauchi, T.

Revision History  

• Version 1.0: 2022-07-06
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2025-04-16
  Changes: Database references, Structure summary