1ID9

STRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[F]U IN PRESENCE OF RH(NH3)6+++


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Destabilizing effect of a fluorouracil extra base in a hybrid RNA duplex compared with bromo and chloro analogues.

Cruse, W.Saludjian, P.Neuman, A.Prange, T.

(2001) Acta Crystallogr.,Sect.D 57: 1609-1613

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In the presence of cobalt, rhodium or iridium hexammine salts, the RNA/DNA hybrid r-GCUUCGGC-d(X)U (with X = F, Cl or Br) crystallizes as a double-stranded helix with four consecutive G-U and C-U mismatches. The deoxy chloro- and bromouracil derivati ...

    In the presence of cobalt, rhodium or iridium hexammine salts, the RNA/DNA hybrid r-GCUUCGGC-d(X)U (with X = F, Cl or Br) crystallizes as a double-stranded helix with four consecutive G-U and C-U mismatches. The deoxy chloro- and bromouracil derivatives are isomorphous, space group C2, unit-cell parameters a = 53.80, b = 19.40, c = 50.31 A, beta = 109.9 degrees, with the same infinite helix arrangement in the packing along the c axis with one extra DNA halogenouracil base included in the stacking. However, the fluorouracil derivative, with unit-cell parameters a = 53.75, b = 19.40, c = 45.84 A, beta = 105.7 degrees, is not isomorphous. The corresponding extra DNA base d(F)U of the second strand is ejected out of the helical stack, leading to a shortening of the c axis. The specific destabilization of the fluorouracil for the duplex building is analyzed in terms of the polarization effect of the halogen atom attached to the 3'-terminal base that modulates its interactions.


    Related Citations: 
    • Structure of a Mispaired RNA Double Helix at 1.6 A Resolution and Implications for the Prediction of RNA Secondary Structure
      Cruse, W.,Saludjian, P.,Biala, E.,Strazewski, P.,Prange, T.,Kennard, O.
      (1994) Proc.Natl.Acad.Sci.USA 91: 4160


    Organizational Affiliation

    CSSB - Chimie Structurale Biomol├ęculaire (UPRES A7031 CNRS), UFR Biom├ędicale 74, Rue Marcel Cachin, 93017 Bobigny CEDEX, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(UFP))-3'A,B9N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
RHD
Query on RHD

Download SDF File 
Download CCD File 
A
RHODIUM HEXAMINE ION
H18 N6 Rh
JGYYKTIOJIEIKU-QTRIFGRDAZ
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UFP
Query on UFP
A, B
DNA LINKINGC9 H12 F N2 O8 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.156 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 53.730α = 90.00
b = 19.390β = 105.70
c = 45.830γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SHELXL-97refinement
CCP4data scaling
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-04-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance