2BJ6

Crystal Structure of a decameric HNA-RNA hybrid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.254 
  • R-Value Work: 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

  • 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: 
    • 1,5-Anhydro-2,3-Dideoxy-2-(Guanin-9-Yl)-D-Arabino-Hexitol
      Declerq, R.,Herdewijn, P.,Vanmeervelt, L.
      (1996) Acta Crystallogr.,Sect.C 52: 1213
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
SYNTHETIC HNAA,B,C,D10Homo sapiens
Entity ID: 2
MoleculeChainsLengthOrganism
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 SDF File 
Download CCD File 
B, C, E, G
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
6HA
Query on 6HA
A, B, C, D
DNA LINKINGC11 H16 N5 O6 PDA
6HG
Query on 6HG
A, B, C, D
DNA LINKINGC11 H16 N5 O7 PDG
6HC
Query on 6HC
A, B, C, D
DNA LINKINGC10 H16 N3 O7 PDC
6HT
Query on 6HT
A, B, C, D
DNA LINKINGC11 H17 N2 O8 PDT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.217 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 113.910α = 90.00
b = 113.910β = 90.00
c = 55.370γ = 90.00
Software Package:
Software NamePurpose
CCP4phasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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