4JIY

RNA three-way junction stabilized by a supramolecular di-iron(II) cylinder drug


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Binding of a designed anti-cancer drug to the central cavity of an RNA three-way junction.

Phongtongpasuk, S.Paulus, S.Schnabl, J.Sigel, R.K.Spingler, B.Hannon, M.J.Freisinger, E.

(2013) Angew Chem Int Ed Engl 52: 11513-11516

  • DOI: https://doi.org/10.1002/anie.201305079
  • Primary Citation of Related Structures:  
    4JIY

  • PubMed Abstract: 

    Getting to the heart of it: Co-crystallization of an RNA three-way junction with a cylindrical di-iron(II)-based anti-cancer drug (green) results in π-stacking interactions between the cylinder and the central base pairs of the RNA structure. The shape, size, and cationic nature of the cylinder were found to be responsible for this perfect fit. Native gel electrophoresis studies confirmed stabilization of the RNA three-way junction by the iron(II) cylinder.


  • Organizational Affiliation

    Institut für Anorganische Chemie, Universität Zürich, Winterthurerstrasse 190, 8057 Zürich (Switzerland) http://www.chem.uzh.ch; School of Chemistry, University of Birmingham, Edgbaston, Birmingham B152TT (UK).


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
5'-(CGUACG)-3'6N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.224 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.745α = 90
b = 45.745β = 90
c = 45.745γ = 90
Software Package:
Software NamePurpose
RemDAqdata collection
SHELXDphasing
SHELXL-97refinement
XDSdata reduction
XPREPdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2013-10-02
    Changes: Database references
  • Version 1.2: 2013-11-06
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations