1IHA

Structure of the Hybrid RNA/DNA R-GCUUCGGC-D[BR]U in Presence of RH(NH3)6+++


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 D Biol Crystallogr 57: 1609-1613

  • DOI: 10.1107/s0907444901012318
  • Primary Citation of Related Structures:  
    1ICG, 1ID9, 1IDW, 1IHA

  • 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 derivatives are isomorphous, space group C2, unit-cell parameters a = 53 ...

    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.B., Saludjian, P., Biala, E., Strazewski, P., Prange, T., Kennard, O.
      (1994) Proc Natl Acad Sci U S A 91: 4160

    Organizational Affiliation

    CSSB - Chimie Structurale Biomoléculaire (UPRES A7031 CNRS), UFR Biomédicale 74, Rue Marcel Cachin, 93017 Bobigny CEDEX, France.



Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(BRU))-3'A, B 9N/A
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RHD
Query on RHD

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
RHODIUM HEXAMINE ION
H18 N6 Rh
JGYYKTIOJIEIKU-QTRIFGRDAZ
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.161 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.8α = 90
b = 19.4β = 109.9
c = 50.31γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
ROTAVATAdata reduction
AMoREphasing
SHELXL-97refinement
CCP4data scaling
ROTAVATAdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-05-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description