4U3O

Octameric RNA duplex soaked in manganese(II)chloride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

The X-ray Structures of Six Octameric RNA Duplexes in the Presence of Different Di- and Trivalent Cations.

Schaffer, M.F.Peng, G.Spingler, B.Schnabl, J.Wang, M.Olieric, V.Sigel, R.K.

(2016) Int J Mol Sci 17

  • DOI: https://doi.org/10.3390/ijms17070988
  • Primary Citation of Related Structures:  
    4U3L, 4U3O, 4U3P, 4U3R, 4U47, 4U78

  • PubMed Abstract: 

    Due to the polyanionic nature of RNA, the principles of charge neutralization and electrostatic condensation require that cations help to overcome the repulsive forces in order for RNA to adopt a three-dimensional structure. A precise structural knowledge of RNA-metal ion interactions is crucial to understand the mechanism of metal ions in the catalytic or regulatory activity of RNA. We solved the crystal structure of an octameric RNA duplex in the presence of the di- and trivalent metal ions Ca(2+), Mn(2+), Co(2+), Cu(2+), Sr(2+), and Tb(3+). The detailed investigation reveals a unique innersphere interaction to uracil and extends the knowledge of the influence of metal ions for conformational changes in RNA structure. Furthermore, we could demonstrate that an accurate localization of the metal ions in the X-ray structures require the consideration of several crystallographic and geometrical parameters as well as the anomalous difference map.


  • Organizational Affiliation

    Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zürich CH-8057, Switzerland. michelle.schaffer@chem.uzh.ch.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*CP*GP*UP*AP*CP*GP*A)-3')
A, B
8synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.328α = 90
b = 46.328β = 90
c = 58.075γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2016-07-13
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description