Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 10.23 kDa 
• Atom Count: 805 
• Modelled Residue Count: 32 
• Deposited Residue Count: 32 
• Unique nucleic acid chains: 2

1R3O

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

• PDB DOI: 10.2210/pdb1R3O/pdb
• NDB: UR0036

• Classification: RNA
• Mutation(s): No 


• Deposited: 2003-10-02 Released: 2003-12-23 
• Deposition Author(s): Vallazza, M., Perbandt, M., Klussmann, S., Rypniewski, W., Erdmann, V.A., Betzel, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.286 
• R-Value Work: 0.239 
• R-Value Observed: 0.241 

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 D Biol Crystallogr 60: 1-7

• PubMed: 14684885 
• DOI: 10.1107/s0907444903027690
• Primary Citation of Related Structures:  
  1R3O


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
L-RNA	A, C	8	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
L-RNA	B, D	8	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.286 
• R-Value Work: 0.239 
• R-Value Observed: 0.241 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.109	α = 90
b = 46.109	β = 90
c = 263.501	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-10-02 
• Released Date: 2003-12-23 
Deposition Author(s): Vallazza, M., Perbandt, M., Klussmann, S., Rypniewski, W., Erdmann, V.A., Betzel, C.

Revision History  

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