413D

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.182 
  • R-Value Observed: 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

  • DOI: 10.1093/nar/27.4.949
  • Primary Citation of Related Structures:  
    413D

  • 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 the presence of the A'-RNA conformation has been found in a single crystal structure for the first time ...

    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

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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R(*UP*GP*AP*GP*CP*UP*UP*CP*GP*GP*CP*UP*C)-3')A 13N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.49α = 90
b = 32.3β = 117.56
c = 38.76γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
RIGAKUdata reduction
RIGAKUdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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