1MME

THE CRYSTAL STRUCTURE OF AN ALL-RNA HAMMERHEAD RIBOZYME: A PROPOSED MECHANISM FOR RNA CATALYTIC CLEAVAGE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage.

Scott, W.G., Finch, J.T., Klug, A.

(1995) Cell 81: 991-1002

  • DOI: 10.1016/s0092-8674(05)80004-2
  • Primary Citation of Related Structures:  
    1MME

  • PubMed Abstract: 

    • We have solved the crystal structure of an all-RNA hammerhead ribozyme having a single 2'-O-methyl cytosine incorporated at the active site to prevent cleavage. The conditions used differ from those in another recent solution in four significant ways: first, it is an all-RNA ribozyme rather than a DNA-RNA hybrid; second, the connectivity of the ribozyme backbone strands is different; third, the crystals were grown in the presence of a much lower concentration of salt; and fourth, the crystal packing scheme is very different ...

    We have solved the crystal structure of an all-RNA hammerhead ribozyme having a single 2'-O-methyl cytosine incorporated at the active site to prevent cleavage. The conditions used differ from those in another recent solution in four significant ways: first, it is an all-RNA ribozyme rather than a DNA-RNA hybrid; second, the connectivity of the ribozyme backbone strands is different; third, the crystals were grown in the presence of a much lower concentration of salt; and fourth, the crystal packing scheme is very different. Nevertheless, the three-dimensional structure of the all-RNA hammerhead ribozyme is similar to the previous structure. Five potential Mg(II)-binding sites are identified, including one positioned near the ribozyme catalytic pocket. Upon this basis, as well as upon comparisons with the metal-binding sites in the structurally homologous uridine turn of tRNAPhe, we propose a mechanism for RNA catalytic cleavage.

    Organizational Affiliation: 

    Medical Research Council, Laboratory of Molecular Biology, Cambridge, England.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    RNA HAMMERHEAD RIBOZYMEA, C16N/A
    Protein Feature View
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    • Reference Sequence
    Find similar nucleic acids by: 
    (by identity cutoff)  |  Structure
    Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA HAMMERHEAD RIBOZYMEB, D25N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.10 Å
    • R-Value Free: 0.293 
    • R-Value Work: 0.251 
    • R-Value Observed: 0.251 
    • Space Group: P 31 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 64.98α = 90
    b = 64.98β = 90
    c = 138.14γ = 120
    Software Package:
    Software NamePurpose
    X-PLORrefinement
    IPMOSFLMdata reduction

    Structure Validation

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    View more in-depth experimental data

    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1996-02-06
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance