2AO5

Crystal structure of an RNA duplex r(GGCGBrUGCGCU)2 with terminal and internal tandem G-U base pairs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of an RNA duplex r(GGCGBrUGCGCU)2 with terminal and internal tandem G.U base pairs.

Utsunomiya, R.Suto, K.Balasundaresan, D.Fukamizu, A.Kumar, P.K.Mizuno, H.

(2006) Acta Crystallogr D Biol Crystallogr 62: 331-338

  • DOI: 10.1107/S0907444905043210
  • Primary Citation of Related Structures:  
    2AO5

  • PubMed Abstract: 
  • The crystal structure of a self-complementary RNA duplex r(GGCG(Br)UGCGCU)(2) with terminal G.U and internal tandem G.U base pairs has been determined at 2.1 Angstroms resolution. The crystals belong to the tetragonal space group P4(3), with unit-cel ...

    The crystal structure of a self-complementary RNA duplex r(GGCG(Br)UGCGCU)(2) with terminal G.U and internal tandem G.U base pairs has been determined at 2.1 Angstroms resolution. The crystals belong to the tetragonal space group P4(3), with unit-cell parameters a = b = 37.69, c = 96.28 Angstroms and two duplexes in the asymmetric unit. The two strands of each duplex are related by a pseudodyad axis. The structure was refined to final R(work) and R(free) values of 20.9 and 25.3%, respectively. The duplexes stack in an end-to-end manner, forming infinite columns along the c axis. This is the first structural study of an RNA duplex containing G.U pairs at the termini. The stacking overlaps of the terminal G.U base pairs with their adjacent Watson-Crick base pairs are larger than those of Watson-Crick base pairs of the 5'-YR-3'/3'-RY-5' type. The terminal G.U base pairs of neighbouring duplexes are also stacked with each other. An alternating underwound-overwound pattern of the twist angles is seen at each step along the duplex. This observation is typical for internal tandem G.U pairs, while the terminal G.U base pairs exhibit high twist angles with the adjacent Watson-Crick pairs. The 3'-side of U of the internal G.U base pair, which is unstacked, appears to be stabilized by pi-cation interaction with an Mg(2+) ion.


    Organizational Affiliation

    Institute of Applied Biochemistry, University of Tsukuba, Ibaraki, Japan.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-R(*GP*GP*CP*GP*(5BU)P*GP*CP*GP*CP*U)-3'A, B, C, D10N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MG
    Query on MG

    Download CCD File 
    A
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.10 Å
    • R-Value Free: 0.250 
    • R-Value Work: 0.207 
    • R-Value Observed: 0.222 
    • Space Group: P 43
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 37.693α = 90
    b = 37.693β = 90
    c = 96.283γ = 90
    Software Package:
    Software NamePurpose
    CNSrefinement
    HKL-2000data reduction
    SCALEPACKdata scaling
    CNSphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2006-03-28
      Type: Initial release
    • Version 1.1: 2008-04-30
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance