2G3S

RNA structure containing GU base pairs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The crystal structure at 1.5 angstroms resolution of an RNA octamer duplex containing tandem G.U basepairs

Jang, S.B.Hung, L.W.Jeong, M.S.Holbrook, E.L.Chen, X.Turner, D.H.Holbrook, S.R.

(2006) Biophys J 90: 4530-4537

  • DOI: https://doi.org/10.1529/biophysj.106.081018
  • Primary Citation of Related Structures:  
    2G3S

  • PubMed Abstract: 

    The crystal structure of the RNA octamer, 5'-GGCGUGCC-3' has been determined from x-ray diffraction data to 1.5 angstroms resolution. In the crystal, this oligonucleotide forms five self-complementary double-helices in the asymmetric unit. Tandem 5'GU/3'UG basepairs comprise an internal loop in the middle of each duplex. The NMR structure of this octameric RNA sequence is also known, allowing comparison of the variation among the five crystallographic duplexes and the solution structure. The G.U pairs in the five duplexes of the crystal form two direct hydrogen bonds and are stabilized by water molecules that bridge between the base of guanine (N2) and the sugar (O2') of uracil. This contrasts with the NMR structure in which only one direct hydrogen bond is observed for the G.U pairs. The reduced stability of the r(CGUG)2 motif relative to the r(GGUC)2 motif may be explained by the lack of stacking of the uracil bases between the Watson-Crick and G.U pairs as observed in the crystal structure.


  • Organizational Affiliation

    Korea Nanobiotechnology Center, Pusan National University, Jangjeon-dong, Keumjeong-gu, Busan, Korea. sbjang@pusan.ac.kr


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3'
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
8synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 26.332α = 112.1
b = 43.998β = 99.03
c = 54.971γ = 89.96
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-01-16
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy