488D

CATALYTIC RNA ENZYME-PRODUCT COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction.

Murray, J.B.Szoke, H.Szoke, A.Scott, W.G.

(2000) Mol Cell 5: 279-287

  • DOI: 10.1016/s1097-2765(00)80423-2
  • Primary Citation of Related Structures:  
    488D

  • PubMed Abstract: 
  • We have determined the crystal structure of the enzyme-product complex of the hammerhead ribozyme by using a reinforced crystal lattice to trap the complex prior to dissociation and by employing X-ray holographic image reconstruction, a real-space electron density imaging and refinement procedure ...

    We have determined the crystal structure of the enzyme-product complex of the hammerhead ribozyme by using a reinforced crystal lattice to trap the complex prior to dissociation and by employing X-ray holographic image reconstruction, a real-space electron density imaging and refinement procedure. Subsequent to catalysis, the cleavage site residue (C-17), together with its 2',3'-cyclic phosphate, adopts a conformation close to and approximately perpendicular to the Watson-Crick base-pairing faces of two highly conserved purines in the ribozyme's catalytic pocket (G-5 and A-6). We observe several interactions with functional groups on these residues that have been identified as critical for ribozyme activity by biochemical analyses but whose role has defied explanation in terms of previous structural analyses. These interactions may therefore be relevant to the hammerhead ribozyme reaction mechanism.


    Organizational Affiliation

    The Center for the Molecular Biology of RNA and Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    RNA RIBOZYME STRANDA16N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      FIRST RNA FRAGMENT OF CLEAVED SUBSTRATEB20N/A
      Protein Feature View
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      • Reference Sequence
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        SECOND RNA FRAGMENT OF CLEAVED SUBSTRATEC5N/A
        Protein Feature View
        Expand
        • Reference Sequence
        Find similar nucleic acids by:  (by identity cutoff)  |  Structure
        Entity ID: 4
        MoleculeChainsLengthOrganismImage
        UNCLEAVED RNA SUBSTRATED25N/A
        Protein Feature View
        Expand
        • Reference Sequence
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 3.10 Å
        • R-Value Free: 0.301 
        • R-Value Work: 0.258 
        • R-Value Observed: 0.258 
        • Space Group: P 31 2 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 65.503α = 90
        b = 65.503β = 90
        c = 136.484γ = 120
        Software Package:
        Software NamePurpose
        X-PLORmodel building
        X-PLORrefinement
        MOSFLMdata reduction
        CCP4data scaling
        X-PLORphasing

        Structure Validation

        View Full Validation Report




        Entry History 

        Deposition Data

        Revision History  (Full details and data files)

        • Version 1.0: 2000-03-06
          Type: Initial release
        • Version 1.1: 2008-04-26
          Changes: Version format compliance
        • Version 1.2: 2011-07-13
          Changes: Version format compliance