409D

CRYSTAL STRUCTURE OF AN RNA R(CCCIUGGG) WITH THREE INDEPENDENT DUPLEXES INCORPORATING TANDEM I.U WOBBLES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of an RNA octamer duplex r(CCCIUGGG)2 incorporating tandem I.U wobbles.

Pan, B.Mitra, S.N.Sun, L.Hart, D.Sundaralingam, M.

(1998) Nucleic Acids Res. 26: 5699-5706


  • PubMed Abstract: 
  • The crystal structure of the RNA octamer duplex r(CCCIUGGG)2has been elucidated at 2.5 A resolution. The crystals belong to the space group P21and have unit cell constants a = 33.44 A, b = 43.41 A, c = 49.39 A and beta = 104.7 degrees with three inde ...

    The crystal structure of the RNA octamer duplex r(CCCIUGGG)2has been elucidated at 2.5 A resolution. The crystals belong to the space group P21and have unit cell constants a = 33.44 A, b = 43.41 A, c = 49.39 A and beta = 104.7 degrees with three independent duplexes (duplexes 1-3) in the asymmetric unit. The structure was solved by the molecular replacement method and refined to an Rwork/Rfree of 0.185/0.243 using 3765 reflections between 8.0 and 2.5 A. This is the first report of an RNA crystal structure incorporating I.U wobbles and three molecules in the asymmetric unit. Duplex 1 displays a kink of 24 degrees between the mismatch sites, while duplexes 2 and 3 have two kinks each of 19 degrees and 27 degrees, and 24 degrees and 29 degrees, respectively, on either side of the tandem mismatches. At the I.U/U.I mismatch steps, duplex 1 has a twist angle of 33.9 degrees, close to the average for all base pair steps, but duplexes 2 and 3 are underwound, with twist angles of 24.4 degrees and 26.5 degrees, respectively. The tandem I.U wobbles show intrastrand purine-pyrimidine stacking but exhibit interstrand purine-purine stacking with the flanking C.G pairs. The three independent duplexes are stacked non-coaxially in a head-to-tail fashion to form infinite pseudo-continuous helical columns which form intercolumn hydrogen bonding interactions through the 2'-hydroxyl groups where the minor grooves come together.


    Organizational Affiliation

    Department of Chemistry and Department of Biochemistry and Biophysics Program, The Ohio State University,Biological Macromolecular Structure Center, Columbus, OH 43210, USA.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*CP*CP*IP*UP*GP*GP*G)-3')A,B,C,D,E,F8N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 33.440α = 90.00
b = 43.410β = 104.70
c = 49.390γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
AMoREphasing
R-AXISdata reduction
R-AXISdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance