1HMH

THREE-DIMENSIONAL STRUCTURE OF A HAMMERHEAD RIBOZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.257 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Three-dimensional structure of a hammerhead ribozyme.

Pley, H.W.Flaherty, K.M.McKay, D.B.

(1994) Nature 372: 68-74

  • DOI: 10.1038/372068a0
  • Primary Citation of Related Structures:  
    1HMH

  • PubMed Abstract: 
  • The hammerhead ribozyme is a small catalytic RNA motif made up of three base-paired stems and a core of highly conserved, non-complementary nucleotides essential for catalysis. The X-ray crystallographic structure of a hammerhead RNA-DNA ribozyme-inhibitor complex at 2 ...

    The hammerhead ribozyme is a small catalytic RNA motif made up of three base-paired stems and a core of highly conserved, non-complementary nucleotides essential for catalysis. The X-ray crystallographic structure of a hammerhead RNA-DNA ribozyme-inhibitor complex at 2.6 A resolution reveals that the base-paired stems are A-form helices and that the core has two structural domains. The first domain is formed by the sequence 5'-CUGA following stem I and is a sharp turn identical to the uridine turn of transfer RNA, whereas the second is a non-Watson-Crick three-base-pair duplex with a divalent-ion binding site. The phosphodiester backbone of the DNA inhibitor strand is splayed out at the phosphate 5' to the cleavage site. The structure indicates that the ribozyme may destabilize a substrate strand in order to facilitate twisting of the substrate to allow cleavage of the scissile bond.


    Related Citations: 
    • Model for an RNA Tertiary Interaction from the Structure of an Intermolecular Complex Between a GAAA Tetraloop and an RNA Helix
      Pley, H.W., Flaherty, K.M., McKay, D.B.
      (1994) Nature 372: 111
    • 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
    • Crystals of a Hammerhead Ribozyme
      Pley, H.W., Lindes, D.S., Deluca-Flaherty, C., McKay, D.B.
      (1993) J Biol Chem 268: 19656

    Organizational Affiliation

    Department of Structural Biology, Stanford University School of Medicine, California 94305-5400.



Macromolecules
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Entity ID: 1
MoleculeChainsLengthOrganismImage
HAMMERHEAD RIBOZYME-RNA STRANDA, C, E 34N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
HAMMERHEAD RIBOZYME-DNA STRANDB, D, F 13N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.257 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.74α = 90
b = 89.74β = 90
c = 185.78γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-12-07
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance