413D

A'-FORM RNA DOUBLE HELIX IN THE SINGLE CRYSTAL STRUCTURE OF R(UGAGCUUCGGCUC)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A'-form RNA double helix in the single crystal structure of r(UGAGCUUCGGCUC).

Tanaka, Y.Fujii, S.Hiroaki, H.Sakata, T.Tanaka, T.Uesugi, S.Tomita, K.Kyogoku, Y.

(1999) Nucleic Acids Res. 27: 949-955


  • PubMed Abstract: 
  • Here we demonstrate the presence of the A'-RNA conformation using the single crystal structure of a tridecamer: r(UGAGCUUCGGCUC). The average A'-RNA conformation deduced from X-ray fiber diffraction data had only been available previously, but now th ...

    Here we demonstrate the presence of the A'-RNA conformation using the single crystal structure of a tridecamer: r(UGAGCUUCGGCUC). The average A'-RNA conformation deduced from X-ray fiber diffraction data had only been available previously, but now the presence of the A'-RNA conformation has been found in a single crystal structure for the first time. Statistical analysis showed that the A'-RNA conformation is distinguishable from the A-RNA conformation in a plot of the major groove width against the base pair inclination angle. The major groove of the A'-RNA conformation is wide enough to accommodate a protein or peptide while that of the A-RNA conformation is too narrow to do so. The presence of the A'-RNA conformation is significant for protein-RNA interaction.


    Related Citations: 
    • Conformational features of the four successive non-Watson-Crick base pairs in RNA duplex
      Fujii, S.,Tanaka, Y.,Uesugi, S.,Tanaka, T.,Sakata, T.,Hiroaki, H.
      (1992) Nucleic Acids Symp.Ser. 27: 63
    • Molecular structure of extraordinarily stable RNA : model building and X-ray analysis
      Fujii, S.,Tanaka, Y.,Tomita, K.-I.,Sakata, T.,Hiroaki, H.,Tanaka, T.,Uesugi, S.
      (1991) Nucleic Acids Symp.Ser. 25: 181


    Organizational Affiliation

    Division of Molecular Biophysics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565, Japan. tanaka@protein.osaka-u.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*GP*AP*GP*CP*UP*UP*CP*GP*GP*CP*UP*C)-3')A13N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 38.490α = 90.00
b = 32.300β = 117.56
c = 38.760γ = 90.00
Software Package:
Software NamePurpose
RIGAKUdata scaling
X-PLORrefinement
RIGAKUdata reduction
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-07-10
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance