483D

CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.11 Å
  • R-Value Free: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The two faces of the Escherichia coli 23 S rRNA sarcin/ricin domain: the structure at 1.11 A resolution.

Correll, C.C.Wool, I.G.Munishkin, A.

(1999) J.Mol.Biol. 292: 275-287

  • DOI: 10.1006/jmbi.1999.3072
  • Primary Citation of Related Structures:  480D

  • PubMed Abstract: 
  • The sarcin/ricin domain of 23 S - 28 S ribosomal RNA is essential for protein synthesis because it forms a critical part of the binding site for elongation factors. A crystal structure of an RNA of 27 nucleotides that mimics the domain in Escherichia ...

    The sarcin/ricin domain of 23 S - 28 S ribosomal RNA is essential for protein synthesis because it forms a critical part of the binding site for elongation factors. A crystal structure of an RNA of 27 nucleotides that mimics the domain in Escherichia coli 23 S rRNA was determined at 1.11 A resolution. The domain folds into a hairpin distorted by four non-canonical base-pairs and one base triple. The fold is stabilized by cross-strand and intra-stand stacking; no intramolecular stabilizing metal ions are observed. This is the first structure to reveal in great detail the geometry and the hydration of two common motifs that are conserved in this rRNA domain, a GAGA tetraloop and a G-bulged cross-strand A stack. Differences in the region connecting these motifs to the stem in the E. coli and in the rat sarcin/ricin domains may contribute to the species-specific binding of elongation factors. Correlation of nucleotide protection data with the structure indicates that the domain has two surfaces. One surface is accessible, lies primarily in the major groove, and is likely to bind the elongation factors. The second lies primarily in the minor groove, and is likely to be buried in the ribosome. This minor groove surface includes the Watson-Crick faces of the cytosine bases in the unusual A2654.C2666 and U2653.C2667 water-mediated base-pairs.


    Related Citations: 
    • The Conformation of the Sarcin/Ricin Loop from 28 S Ribosomal RNA
      Szewczak, A.A.,Moore, P.B.
      (1993) Proc.Natl.Acad.Sci.USA 90: 9581
    • Comparison of the Crystal and Solution Structures of Two RNA Oligonucleotides
      Rife, J.P.,Stallings, S.G.,Correll, C.C.,Dallas, A.,Steitz, T.A.,Moore, P.B.
      (1999) Biophys.J. 76: 65
    • The Sarcin/Ricin Loop, a Modular RNA
      Szewczak, A.A.,Moore, P.B.
      (1995) J.Mol.Biol. 247: 81
    • Crystal Structure of the Ribosomal RNA Domain Essential for Binding Elongation Factors
      Correll, C.C.,Munishkin, A.,Chan, Y.-L.,Ren, Z.,Wool, I.G.
      (1998) Proc.Natl.Acad.Sci.USA 95: 13436


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA. ccorrell@midway.uchicago.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
SARCIN/RICIN RRNA DOMAINA27N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.11 Å
  • R-Value Free: 0.202 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 29.481α = 90.00
b = 29.481β = 90.00
c = 76.353γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-10-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance