1GID

CRYSTAL STRUCTURE OF A GROUP I RIBOZYME DOMAIN: PRINCIPLES OF RNA PACKING


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a group I ribozyme domain: principles of RNA packing.

Cate, J.H.Gooding, A.R.Podell, E.Zhou, K.Golden, B.L.Kundrot, C.E.Cech, T.R.Doudna, J.A.

(1996) Science 273: 1678-1685


  • PubMed Abstract: 
  • Group I self-splicing introns catalyze their own excision from precursor RNAs by way of a two-step transesterification reaction. The catalytic core of these ribozymes is formed by two structural domains. The 2.8-angstrom crystal structure of one of t ...

    Group I self-splicing introns catalyze their own excision from precursor RNAs by way of a two-step transesterification reaction. The catalytic core of these ribozymes is formed by two structural domains. The 2.8-angstrom crystal structure of one of these, the P4-P6 domain of the Tetrahymena thermophila intron, is described. In the 160-nucleotide domain, a sharp bend allows stacked helices of the conserved core to pack alongside helices of an adjacent region. Two specific long-range interactions clamp the two halves of the domain together: a two-Mg2+-coordinated adenosine-rich corkscrew plugs into the minor groove of a helix, and a GAAA hairpin loop binds to a conserved 11-nucleotide internal loop. Metal- and ribose-mediated backbone contacts further stabilize the close side-by-side helical packing. The structure indicates the extent of RNA packing required for the function of large ribozymes, the spliceosome, and the ribosome.


    Related Citations: 
    • Metal-Binding Sites in the Major Groove of a Large Ribozyme Domain
      Cate, J.H.,Doudna, J.A.
      (1996) Structure 4: 1221
    • RNA Tertiary Structure Mediation by Adenosine
      Cate, J.H.,Gooding, A.R.,Podell, E.,Zhou, K.,Golden, B.L.,Szewczak, A.A.,Kundrot, C.E.,Cech, T.R.,Doudna, J.A.
      (1996) Science 273: 1696


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. doudna@csb.yale.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
P4-P6 RNA RIBOZYME DOMAINA,B158synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NCO
Query on NCO

Download SDF File 
Download CCD File 
A, B
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.800α = 90.00
b = 128.700β = 90.00
c = 145.900γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CCP4data scaling
DENZOdata reduction
X-PLORrefinement
MAD-SIRmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-12-31
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance