7EIA | pdb_00007eia

RNA kink-turn motif with pyrrolo cytosine

• PDB DOI: https://doi.org/10.2210/pdb7EIA/pdb
• NAKB: 7EIA

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


• Deposited: 2021-03-30 Released: 2022-03-30 
• 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: 
  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.207 (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)

Macromolecule Content 

• Total Structure Weight: 50.05 kDa 
• Atom Count: 3,317 
• Modeled Residue Count: 152 
• Deposited Residue Count: 152 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(4PC))-R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')	A, B, C, D, E, F, G, H	19	synthetic construct

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.056	α = 90
b = 77.575	β = 90
c = 81.013	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-03-30 
Deposition Author(s): Kondo, J., Miyauchi, T.

Revision History  

• Version 1.0: 2022-03-30
  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