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 

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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