1RMN

A THREE-DIMENSIONAL MODEL FOR THE HAMMERHEAD RIBOZYME BASED ON FLUORESCENCE MEASUREMENTS


Experimental Data Snapshot

  • Method: FLUORESCENCE TRANSFER

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements.

Tuschl, T.Gohlke, C.Jovin, T.M.Westhof, E.Eckstein, F.

(1994) Science 266: 785-789


  • PubMed Abstract: 
  • For the understanding of the catalytic function of the RNA hammerhead ribozyme, a three-dimensional model is essential but neither a crystal nor a solution structure has been available. Fluorescence resonance energy transfer (FRET) was used to study ...

    For the understanding of the catalytic function of the RNA hammerhead ribozyme, a three-dimensional model is essential but neither a crystal nor a solution structure has been available. Fluorescence resonance energy transfer (FRET) was used to study the structure of the ribozyme in solution in order to establish the relative spatial orientation of the three constituent Watson-Crick base-paired helical segments. Synthetic constructs were labeled with the fluorescence donor (5-carboxyfluorescein) and acceptor (5-carboxytetramethylrhodamine) located at the ends of the strands constituting the ribozyme molecule. The acceptor helix in helix pairs I and III and in II and III was varied in length from 5 to 11 and 5 to 9 base pairs, respectively, and the FRET efficiencies were determined and correlated with a reference set of labeled RNA duplexes. The FRET efficiencies were predicted on the basis of vector algebra analysis, as a function of the relative helical orientations in the ribozyme constructs, and compared with experimental values. The data were consistent with a Y-shaped arrangement of the ribozyme with helices I and II in close proximity and helix III pointing away. These orientational constraints were used for molecular modeling of a three-dimensional structure of the complete ribozyme.


    Organizational Affiliation

    Max-Planck-Institut für Experimentelle Medizin, Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (49-MER)A49N/A
Experimental Data & Validation

Experimental Data

  • Method: FLUORESCENCE TRANSFER
Software Package:
Software NamePurpose
NUCLSQrefinement
NUCLIN/NUCLSQrefinement
NUCLINrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-01-26
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance