3MJB

Cricket Paralysis Virus IGR IRES Domain 3 RNA bound to sulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.242 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification and characterization of anion binding sites in RNA.

Kieft, J.S.Chase, E.Costantino, D.A.Golden, B.L.

(2010) RNA 16: 1118-1123

  • DOI: 10.1261/rna.2072710
  • Primary Citation of Related Structures:  
    3MJ3, 3MJA, 3MJB

  • PubMed Abstract: 
  • Although RNA molecules are highly negatively charged, anions have been observed bound to RNA in crystal structures. It has been proposed that anion binding sites found within isolated RNAs represent regions of the molecule that could be involved in intermolecular interactions, indicating potential contact points for negatively charged amino acids from proteins or phosphate groups from an RNA ...

    Although RNA molecules are highly negatively charged, anions have been observed bound to RNA in crystal structures. It has been proposed that anion binding sites found within isolated RNAs represent regions of the molecule that could be involved in intermolecular interactions, indicating potential contact points for negatively charged amino acids from proteins or phosphate groups from an RNA. Several types of anion binding sites have been cataloged based on available structures. However, currently there is no method for unambiguously assigning anions to crystallographic electron density, and this has precluded more detailed analysis of RNA-anion interaction motifs and their significance. We therefore soaked selenate into two different types of RNA crystals and used the anomalous signal from these anions to identify binding sites in these RNA molecules unambiguously. Examination of these sites and comparison with other suspected anion binding sites reveals features of anion binding motifs, and shows that selenate may be a useful tool for studying RNA-anion interactions.


    Organizational Affiliation

    Howard Hughes Medical Institute and Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA. Jeffrey.Kieft@ucdenver.edu



Macromolecules
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Entity ID: 1
MoleculeChainsLengthOrganismImage
Domain 3 of the cricket paralysis virus intergenic region IRES RNAA 29N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*UP*AP*AP*GP*AP*AP*AP*UP*UP*UP*AP*CP*CP*U)-3')B 14N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.242 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.94α = 90
b = 58.94β = 90
c = 99.37γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance