1GID

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.242 
  • R-Value Observed: 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

  • DOI: 10.1126/science.273.5282.1678
  • Primary Citation of Related Structures:  
    1GID

  • 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 these, the P4-P6 domain of the Tetrahymena thermophila intron, is described ...

    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: 
    • 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
    • Metal-Binding Sites in the Major Groove of a Large Ribozyme Domain
      Cate, J.H., Doudna, J.A.
      (1996) Structure 4: 1221

    Organizational Affiliation

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



Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
P4-P6 RNA RIBOZYME DOMAINA, B158synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NCO
Query on NCO

Download Ideal Coordinates CCD File 
CA [auth B],
DA [auth B],
O [auth A],
P [auth A]
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth B],
BA [auth B],
C [auth A],
D [auth A],
E [auth A],
AA [auth B],
BA [auth B],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.8α = 90
b = 128.7β = 90
c = 145.9γ = 90
Software Package:
Software NamePurpose
MAD-SIRmodel building
X-PLORrefinement
DENZOdata reduction
CCP4data scaling
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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