1R3O

Crystal structure of the first RNA duplex in L-conformation at 1.9A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

First look at RNA in L-configuration.

Vallazza, M.Perbandt, M.Klussmann, S.Rypniewski, W.Einspahr, H.M.Erdmann, V.A.Betzel, C.h.

(2004) Acta Crystallogr.,Sect.D 60: 1-7


  • PubMed Abstract: 
  • Nucleic acid molecules in the mirror image or L-configuration are unknown in nature and are extraordinarily resistant to biological degradation. The identification of functional L-oligonucleotides called Spiegelmers offers a novel approach for drug d ...

    Nucleic acid molecules in the mirror image or L-configuration are unknown in nature and are extraordinarily resistant to biological degradation. The identification of functional L-oligonucleotides called Spiegelmers offers a novel approach for drug discovery based on RNA. The sequence r(CUGGGCGG).r(CCGCCUGG) was chosen as a model system for structural analysis of helices in the L-configuration as the structure of the D-form of this sequence has previously been determined in structural studies of 5S RNA domains, in particular domain E of the Thermus flavus 5S rRNA [Perbandt et al. (2001), Acta Cryst. D57, 219-224]. Unexpectedly, the results of crystallization trials showed little similarity between the D- and the L-forms of the duplex in either the crystallization hits or the diffraction performance. The crystal structure of this L-RNA duplex has been determined at 1.9 A resolution with R(work) and R(free) of 23.8 and 28.6%, respectively. The crystals belong to space group R32, with unit-cell parameters a = 45.7, c = 264.6 A. Although there are two molecules in the asymmetric unit rather than one, the structure of the L-form arranges helical pairs in a head-to-tail fashion to form pseudo-continuous infinite helices in the crystal as in the D-form. On the other hand, the wobble-like G.C(+) base pair seen in the D-RNA analogue does not appear in the L-RNA duplex, which forms a regular double-helical structure with typical Watson-Crick base pairing.


    Organizational Affiliation

    Institutes of Biology, Chemistry and Pharmacy, Free University of Berlin, Biochemistry: Thielallee 63, 14195 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
L-RNAA,C8N/A
Entity ID: 2
MoleculeChainsLengthOrganism
L-RNAB,D8N/A
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
0G
Query on 0G
A, B, C, D
L-RNA LINKINGC10 H14 N5 O8 P

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0C
Query on 0C
A, B, C, D
L-RNA LINKINGC9 H14 N3 O8 P

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0U
Query on 0U
A, B, C, D
L-RNA LINKINGC9 H13 N2 O9 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.239 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 46.109α = 90.00
b = 46.109β = 90.00
c = 263.501γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-23
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation