379D

THE STRUCTURAL BASIS OF HAMMERHEAD RIBOZYME SELF-CLEAVAGE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 

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This is version 1.4 of the entry. See complete history. 


Literature

The structural basis of hammerhead ribozyme self-cleavage.

Murray, J.B., Terwey, D.P., Maloney, L., Karpeisky, A., Usman, N., Beigelman, L., Scott, W.G.

(1998) Cell 92: 665-673

  • DOI: https://doi.org/10.1016/s0092-8674(00)81134-4
  • Primary Citation of Related Structures:  
    379D

  • PubMed Abstract: 

    We have captured an 8.7 A conformational change that takes place in the cleavage site of the hammerhead ribozyme during self-cleavage, using X-ray crystallography combined with physical and chemical trapping techniques. This rearrangement brings the hammerhead ribozyme from the ground state into a conformation that is poised to form the transition state geometry required for hammerhead RNA self-cleavage. Use of a 5'-C-methylated ribose adjacent to the cleavage site permits this ordinarily transient conformational change to be kinetically trapped and observed crystallographically after initiating the hammerhead ribozyme reaction in the crystal. Cleavage of the corresponding unmodified hammerhead ribozyme in the crystal under otherwise identical conditions is faster than in solution, indicating that we have indeed trapped a catalytically relevant intermediate form of this RNA enzyme.

    • Organizational Affiliation: 

    Department of Chemistry, Indiana University, Bloomington 47405, USA.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*UP*GP*GP*UP*CP*UP*GP*AP*UP*GP*AP*GP*GP*CP*C)-3')16N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*GP*CP*CP*GP*AP*AP*AP*CP*UP*CP*GP*UP*AP*AP*GP*A P*GP*UP*CP*AP*CP*CP*AP*C)-3')25N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.1α = 90
b = 65.1β = 90
c = 138.7γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-02-11
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description