1Q96

Crystal structure of a mutant of the sarcin/ricin domain from rat 28S rRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The common and distinctive features of the bulged-G motif based on a 1.04 A resolution RNA structure

Correll, C.C.Beneken, J.Plantinga, M.J.Lubbers, M.Chan, Y.L.

(2003) Nucleic Acids Res. 31: 6806-6818

  • Primary Citation of Related Structures:  1Q93, 1Q9A

  • PubMed Abstract: 
  • Bulged-G motifs are ubiquitous internal RNA loops that provide specific recognition sites for proteins and RNAs. To establish the common and distinctive features of the motif we determined the structures of three variants and compared them with relat ...

    Bulged-G motifs are ubiquitous internal RNA loops that provide specific recognition sites for proteins and RNAs. To establish the common and distinctive features of the motif we determined the structures of three variants and compared them with related structures. The variants are 27-nt mimics of the sarcin/ricin loop (SRL) from Escherichia coli 23S ribosomal RNA that is an essential part of the binding site for elongation factors (EFs). The wild-type SRL has now been determined at 1.04 A resolution, supplementing data obtained before at 1.11 A and allowing the first calculation of coordinate error for an RNA motif. The other two structures, having a viable (C2658U*G2663A) or a lethal mutation (C2658G*G2663C), were determined at 1.75 and 2.25 A resolution, respectively. Comparisons reveal that bulged-G motifs have a common hydration and geometry, with flexible junctions at flanking structural elements. Six conserved nucleotides preserve the fold of the motif; the remaining seven to nine vary in sequence and alter contacts in both grooves. Differences between accessible functional groups of the lethal mutation and those of the viable mutation and wild-type SRL may account for the impaired elongation factor binding to ribosomes with the C2658G*G2663C mutation and may underlie the lethal phenotype.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
sarcin/ricin 28S rRNAA,B,C27N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.201 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 42.246α = 90.00
b = 42.246β = 90.00
c = 336.915γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
HKL-2000data collection
HKL-2000data reduction
EPMRphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-25
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance