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 and a strand, which is fully modified to contain a six-membered ring instead of ribose ...

    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   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
SYNTHETIC HNAA, B, C, D 10Homo sapiens
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(*GP*GP*CP*AP*UP*UP*AP*CP*GP*GP)-3'E, F, G, H 10Homo sapiens
Protein Feature View
Expand
  • Reference Sequence
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  (Full details and data files)

  • 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