2BJ6

Crystal Structure of a decameric HNA-RNA hybrid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Reinforced Hna Backbone Hydration in the Crystal Structure of a Decameric Hna/RNA Hybrid

Maier, T.Przylas, I.Strater, N.Herdewijn, P.Saenger, W.

(2005) J Am Chem Soc 127: 2937

  • DOI: 10.1021/ja045843v
  • Primary Citation of Related Structures:  
    2BJ6

  • PubMed Abstract: 
  • The crystal structure of a decameric HNA/RNA (HNA = 2',3'-dideoxy-1',5'-anhydro-d-arabinohexitol nucleic acid) hybrid with the RNA sequence 5'-GGCAUUACGG-3' is the first crystal structure of a hybrid duplex between a naturally occurring nucleic acid ...

    The crystal structure of a decameric HNA/RNA (HNA = 2',3'-dideoxy-1',5'-anhydro-d-arabinohexitol nucleic acid) hybrid with the RNA sequence 5'-GGCAUUACGG-3' is the first crystal structure of a hybrid duplex between a naturally occurring nucleic acid and a strand, which is fully modified to contain a six-membered ring instead of ribose. The presence of four duplex helices in the asymmetric unit allows for a detailed discussion of hydration, which revealed a tighter spinelike backbone hydration for the HNA- than for the RNA-strands. The reinforced backbone hydration is suggested to contribute significantly to the exceptional stability of HNA-containing duplexes and might be one of the causes for the evolutionary preference for ribose-derived nucleic acids.


    Related Citations: 
    • Molecular Dynamics Simulation to Inverstigate Differences in Minor Groove Hydration of Hna-RNA Hybrids as Compared to Hna-DNA Complexes
      Dewinter, H., Lescrinier, E., Vanaerschot, A., Herdewijn, P.
      (1998) J Am Chem Soc 120: 5381
    • Solution Structure of a Hna-RNA Hybrid
      Lescrinier, E., Esnouf, R., Schraml, J., Busson, R., Heus, H.A., Hilbers, C.W., Herdewijn, P.
      (2000) Chem Biol 7: 719
    • Crystal Structure of Double Helical Hexitol Nucleic Acids
      Declercq, R., Vanaerschot, A., Read, R.J., Herdewijn, P., Vanmeervelt, L.
      (2002) J Am Chem Soc 124: 928
    • 1,5-Anhydro-2,3-Dideoxy-2-(Guanin-9-Yl)-D-Arabino-Hexitol
      Declerq, R., Herdewijn, P., Vanmeervelt, L.
      (1996) Acta Crystallogr C 52: 1213

    Organizational Affiliation

    Institut für Chemie der Freien Universität Berlin, Takustrasse 6, 14195 Berlin, Germany.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    SYNTHETIC HNAA, B, C, D10Homo sapiens
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-R(*GP*GP*CP*AP*UP*UP*AP*CP*GP*GP)-3'E, F, G, H10Homo sapiens
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      SO4
      Query on SO4

      Download CCD File 
      B, C, E, G
      SULFATE ION
      O4 S
      QAOWNCQODCNURD-UHFFFAOYSA-L
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.60 Å
      • R-Value Free: 0.254 
      • R-Value Work: 0.217 
      • R-Value Observed: 0.217 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 113.91α = 90
      b = 113.91β = 90
      c = 55.37γ = 90
      Software Package:
      Software NamePurpose
      CNSrefinement
      DENZOdata reduction
      SCALEPACKdata scaling
      CCP4phasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2005-03-09
        Type: Initial release
      • Version 1.1: 2011-05-08
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance