3MJ3

Cricket Paralysis Virus IGR IRES Domain 3 RNA bound to selenate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.227 

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:  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 i ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Domain 3 of the cricket paralysis virus intergenic region IRES RNAB29N/A
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*AP*AP*GP*AP*AP*AP*UP*UP*UP*AP*CP*CP*U)-3')C14N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SE4
Query on SE4

Download SDF File 
Download CCD File 
B, C
SELENATE ION
O4 Se
QYHFIVBSNOWOCQ-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.227 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.260α = 90.00
b = 59.260β = 90.00
c = 99.775γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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