1J6S

Crystal Structure of an RNA Tetraplex (UGAGGU)4 with A-tetrads, G-tetrads, U-tetrads and G-U octads


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of an RNA purine-rich tetraplex containing adenine tetrads: implications for specific binding in RNA tetraplexes

Pan, B.Xiong, Y.Shi, K.Deng, J.Sundaralingam, M.

(2003) Structure 11: 815-823

  • DOI: 10.1016/s0969-2126(03)00107-2
  • Primary Citation of Related Structures:  
    1J6S

  • PubMed Abstract: 
  • Purine-rich regions in DNA and RNA may contain both guanines and adenines, which have various biological functions. Here we report the crystal structure of an RNA purine-rich fragment containing both guanine and adenine at 1.4 A resolution. Adenines ...

    Purine-rich regions in DNA and RNA may contain both guanines and adenines, which have various biological functions. Here we report the crystal structure of an RNA purine-rich fragment containing both guanine and adenine at 1.4 A resolution. Adenines form an adenine tetrad in the N6-H em leader N7 conformation. Substitution of an adenine tetrad in the guanine tetraplex does not change the global conformation but introduces irregularity in both the hydrogen bonding interaction pattern in the groove and the metal ion binding pattern in the central cavity of the tetraplex. The irregularity in groove binding may be critical for specific binding in tetraplexes. The formation of G-U octads provides a mechanism for interaction in the groove. Ba(2+) ions prefer to bind guanine tetrads, and adenine tetrads can only be bound by Na(+) ions, illustrating the binding selectivity of metal ions for the tetraplex.


    Organizational Affiliation

    Departments of Chemistry and Biochemistry, The Ohio State University, 200 Johnston Lab, 176 West 19th Avenue, Columbus, OH 43210, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-R(*(BRUP*GP*AP*GP*GP*U)-3'A, B, C, D6N/A
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    BA
    Query on BA

    Download CCD File 
    A, B, C, D
    BARIUM ION
    Ba
    XDFCIPNJCBUZJN-UHFFFAOYSA-N
     Ligand Interaction
    NA
    Query on NA

    Download CCD File 
    A, B, C, D
    SODIUM ION
    Na
    FKNQFGJONOIPTF-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.40 Å
    • R-Value Free: 0.184 
    • R-Value Work: 0.166 
    • Space Group: P 4 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 37.984α = 90
    b = 37.984β = 90
    c = 82.195γ = 90
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SOLVEphasing
    RESOLVEmodel building
    CNSrefinement
    RESOLVEphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2003-08-05
      Type: Initial release
    • Version 1.1: 2008-04-26
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance