430D

STRUCTURE OF SARCIN/RICIN LOOP FROM RAT 28S RRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.280 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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.Steitz, T.A.

(1998) Proc.Natl.Acad.Sci.USA 95: 13436-13441


  • PubMed Abstract: 
  • The structure of a 29-nucleotide RNA containing the sarcin/ricin loop (SRL) of rat 28 S rRNA has been determined at 2.1 A resolution. Recognition of the SRL by elongation factors and by the ribotoxins, sarcin and ricin, requires a nearly universal do ...

    The structure of a 29-nucleotide RNA containing the sarcin/ricin loop (SRL) of rat 28 S rRNA has been determined at 2.1 A resolution. Recognition of the SRL by elongation factors and by the ribotoxins, sarcin and ricin, requires a nearly universal dodecamer sequence that folds into a G-bulged cross-strand A stack and a GAGA tetraloop. The juxtaposition of these two motifs forms a distorted hairpin structure that allows direct recognition of bases in both grooves as well as recognition of nonhelical backbone geometry and two 5'-unstacked purines. Comparisons with other RNA crystal structures establish the cross-strand A stack and the GNRA tetraloop as defined and modular RNA structural elements. The conserved region at the top is connected to the base of the domain by a region presumed to be flexible because of the sparsity of stabilizing contacts. Although the conformation of the SRL RNA previously determined by NMR spectroscopy is similar to the structure determined by x-ray crystallography, significant differences are observed in the "flexible" region and to a lesser extent in the G-bulged cross-strand A stack.


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


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
SARCIN/RICIN LOOP FROM RAT 28S R-RNAA29Rattus norvegicus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CBV
Query on CBV
A
RNA LINKINGC9 H13 Br N3 O8 PC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.280 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 56.830α = 90.00
b = 56.830β = 90.00
c = 107.960γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
CCP4data scaling
MLPHAREphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-07
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-05-03
    Type: Source and taxonomy, Structure summary