480D

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 

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
  • Structures With Same Primary Citation

  • 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: 
    • 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 U S A 95: 13436
    • 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
    • The conformation of the sarcin/ricin loop from 28 S ribosomal RNA
      Szewczak, A.A., Moore, P.B.
      (1993) Proc Natl Acad Sci U S A 90: 9581

    Organizational Affiliation

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



Macromolecules

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
SARCIN/RICIN DOMAIN FROM 23 S RRNAA27N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.95α = 90
b = 29.95β = 90
c = 76.42γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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