430D

STRUCTURE OF SARCIN/RICIN LOOP FROM RAT 28S RRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.280 
  • R-Value Observed: 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 U S A 95: 13436-13441

  • DOI: 10.1073/pnas.95.23.13436
  • Primary Citation of Related Structures:  
    430D

  • 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 dodecamer sequence that folds into a G-bulged cross-strand A stack and a GAGA tetraloop ...

    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 U S A 90: 9581
    • The Sarcin/Ricin Loop, a Modular RNA
      Szewczak, A.A., Moore, P.B.
      (1995) J Mol Biol 247: 81
    • 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 --: --

    Organizational Affiliation

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



Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
SARCIN/RICIN LOOP FROM RAT 28S R-RNAA29Rattus norvegicus
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A] , C [auth A] , D [auth A] , E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , 
B [auth A],  C [auth A],  D [auth A],  E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.280 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.83α = 90
b = 56.83β = 90
c = 107.96γ = 120
Software Package:
Software NamePurpose
MLPHAREphasing
CNSrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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