2AWE

Base-Tetrad Swapping Results in Dimerization of RNA Quadruplexes: Implications for Formation of I-Motif RNA Octaplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Base-tetrad swapping results in dimerization of RNA quadruplexes: implications for formation of the i-motif RNA octaplex.

Pan, B.Shi, K.Sundaralingam, M.

(2006) Proc Natl Acad Sci U S A 103: 3130-3134

  • DOI: 10.1073/pnas.0507730103
  • Primary Citation of Related Structures:  
    2AWE

  • PubMed Abstract: 
  • Nucleic acids adopt different multistranded helical architectures to perform various biological functions. Here, we report a crystal structure of an RNA quadruplex containing "base-tetrad swapping" and bulged nucleotide at 2.1-Angstroms resolution. T ...

    Nucleic acids adopt different multistranded helical architectures to perform various biological functions. Here, we report a crystal structure of an RNA quadruplex containing "base-tetrad swapping" and bulged nucleotide at 2.1-Angstroms resolution. The base-tetrad swapping results in a dimer of quadruplexes with an intercalated octaplex fragment at the 5' end junction. The intercalated base tetrads provide the basic repeat unit for constructing a model of intercalated RNA octaplex. The model we obtained shows fundamentally different characteristics from duplex, triplex, and quadruplex. We also observed two different orientations of bulged uridine residues that are related to the interaction with surroundings. This structural evidence reflects the conformational flexibility of bulged nucleotides in RNA quadruplexes and implies the potential roles of bulged nucleotides as recognition and interaction sites in RNA-protein and RNA-RNA interactions.


    Organizational Affiliation

    Department of Chemistry, Ohio State University, 200 Johnston Laboratory, Columbus, 43210-1002, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-R(*UP*(BGM)P*GP*UP*GP*U)-3'A, B, C, D, E, F, G, H6N/A
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SR
    Query on SR

    Download CCD File 
    A
    STRONTIUM ION
    Sr
    PWYYWQHXAPXYMF-UHFFFAOYSA-N
     Ligand Interaction
    K
    Query on K

    Download CCD File 
    A, C, E, F, G
    POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.10 Å
    • R-Value Free: 0.228 
    • R-Value Work: 0.172 
    • R-Value Observed: 0.174 
    • Space Group: I 41 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 82.667α = 90
    b = 82.667β = 90
    c = 74.154γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    DENZOdata reduction
    SCALEPACKdata scaling
    SOLVEphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2006-02-07
      Type: Initial release
    • Version 1.1: 2008-05-01
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance