283D

A CURVED RNA HELIX INCORPORATING AN INTERNAL LOOP WITH G-A AND A-A NON-WATSON-CRICK BASE PAIRING


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A curved RNA helix incorporating an internal loop with G.A and A.A non-Watson-Crick base pairing.

Baeyens, K.J.De Bondt, H.L.Pardi, A.Holbrook, S.R.

(1996) Proc Natl Acad Sci U S A 93: 12851-12855

  • DOI: 10.1073/pnas.93.23.12851
  • Primary Citation of Related Structures:  
    283D

  • PubMed Abstract: 
  • The crystal structure of the RNA dodecamer 5'-GGCC(GAAA)GGCC-3' has been determined from x-ray diffraction data to 2.3-A resolution. In the crystal, these oligomers form double helices around twofold symmetry axes. Four consecutive non-Watson-Crick base pairs make up an internal loop in the middle of the duplex, including sheared G ...

    The crystal structure of the RNA dodecamer 5'-GGCC(GAAA)GGCC-3' has been determined from x-ray diffraction data to 2.3-A resolution. In the crystal, these oligomers form double helices around twofold symmetry axes. Four consecutive non-Watson-Crick base pairs make up an internal loop in the middle of the duplex, including sheared G.A pairs and novel asymmetric A.A pairs. This internal loop sequence produces a significant curvature and narrowing of the double helix. The helix is curved by 34 degrees from end to end and the diameter is narrowed by 24% in the internal loop. A Mn2+ ion is bound directly to the N7 of the first guanine in the Watson-Crick region following the internal loop and the phosphate of the preceding residue. This Mn2+ location corresponds to a metal binding site observed in the hammerhead catalytic RNA.


    Organizational Affiliation

    Structural Biology Division, Lawrence Berkeley National Laboratory, University of California, Berkeley 94720, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*GP*GP*CP*CP*GP*AP*AP*AP*GP*GP*CP*C)-3')A12N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MN
    Query on MN

    Download Ideal Coordinates CCD File 
    B [auth A]MANGANESE (II) ION
    Mn
    WAEMQWOKJMHJLA-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.30 Å
    • R-Value Free: 0.198 
    • R-Value Work: 0.186 
    • R-Value Observed: 0.186 
    • Space Group: P 65 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 37.71α = 90
    b = 37.71β = 90
    c = 88.3γ = 120
    Software Package:
    Software NamePurpose
    X-PLORrefinement
    R-AXISdata reduction
    AMoREphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1996-09-30
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance