472D

STRUCTURE OF AN OCTAMER RNA WITH TANDEM GG/UU MISPAIRS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

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This is version 1.3 of the entry. See complete history


Literature

Synthesis and crystal structure of an octamer RNA r(guguuuac)/r(guaggcac) with G.G/U.U tandem wobble base pairs: comparison with other tandem G.U pairs.

Deng, J.Sundaralingam, M.

(2000) Nucleic Acids Res 28: 4376-4381

  • DOI: https://doi.org/10.1093/nar/28.21.4376
  • Primary Citation of Related Structures:  
    472D

  • PubMed Abstract: 

    We have determined the crystal structure of the RNA octamer duplex r(guguuuac)/r(guaggcac) with a tandem wobble pair, G.G/U.U (motif III), to compare it with U.G/G.U (motif I) and G.U/U.G (motif II) and to better understand their relative stabilities. The crystal belongs to the rhombohedral space group R3. The hexagonal unit cell dimensions are a = b = 41.92 A, c = 56.41 A, and gamma = 120 degrees, with one duplex in the asymmetric unit. The structure was solved by the molecular replacement method at 1.9 A resolution and refined to a final R: factor of 19.9% and R(free) of 23.3% for 2862 reflections in the resolution range 10.0-1.9 A with F >/= 2sigma(F). The final model contains 335 atoms for the RNA duplex and 30 water molecules. The A-RNA stacks in the familiar head-to-tail fashion forming a pseudo-continuous helix. The uridine bases of the tandem U.G pairs have slipped towards the minor groove relative to the guanine bases and the uridine O2 atoms form bifurcated hydrogen bonds with the N1 and N2 of guanines. The N2 of guanine and O2 of uridine do not bridge the 'locked' water molecule in the minor groove, as in motifs I and II, but are bridged by water molecules in the major groove. A comparison of base stacking stabilities of motif III with motifs I and II confirms the result of thermodynamic studies, motif I > motif III > motif II.


  • Organizational Affiliation

    Department of Chemistry, Biological Macromolecular Structure Center, The Ohio State University, 012 Rightmire Hall, 1060 Carmack Road, Columbus, OH 43210-1002, USA.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*UP*GP*UP*UP*UP*AP*C)-3')8N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*UP*AP*GP*GP*CP*AP*C)-3')8N/A
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.92α = 90
b = 41.92β = 90
c = 56.41γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-11-27
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references