1HMH

THREE-DIMENSIONAL STRUCTURE OF A HAMMERHEAD RIBOZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.305 
  • R-Value Work: 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

  • 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-inh ...

    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: 
    • Crystals of a Hammerhead Ribozyme
      Pley, H.W.,Lindes, D.S.,Deluca-Flaherty, C.,McKay, D.B.
      (1993) J.Biol.Chem. 268: 19656
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
HAMMERHEAD RIBOZYME-RNA STRANDA,C,E34N/A
Entity ID: 2
MoleculeChainsLengthOrganism
HAMMERHEAD RIBOZYME-DNA STRANDB,D,F13N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.257 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 89.740α = 90.00
b = 89.740β = 90.00
c = 185.780γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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