Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9.07 kDa 
• Atom Count: 711 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

469D

CRYSTAL STRUCTURE AND IMPROVED ANTISENSE PROPERTIES OF 2'-O-(2-METHOXYETHYL)-RNA

• PDB DOI: 10.2210/pdb469D/pdb
• NDB: AR0015

• Classification: RNA
• Mutation(s): No 


• Deposited: 1999-04-29 Released: 1999-05-12 
• Deposition Author(s): Teplova, M., Minasov, G., Tereshko, V., Inamati, G., Cook, P.D., Egli, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.258 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 

Literature

Crystal structure and improved antisense properties of 2'-O-(2-methoxyethyl)-RNA.

Teplova, M., Minasov, G., Tereshko, V., Inamati, G.B., Cook, P.D., Manoharan, M., Egli, M.

(1999) Nat Struct Biol 6: 535-539

• PubMed: 10360355 
• DOI: 10.1038/9304
• Primary Citation of Related Structures:  
  468D, 469D, 470D, 471D


• PubMed Abstract: 
  

2'-O-(2-Methoxyethyl)-RNA (MOE-RNA) is a nucleic acid analog with promising features for antisense applications. Compared with phosphorothioate DNA (PS-DNA), the MOE modification offers improved nuclease resistance, enhanced RNA affinity, improved cellular uptake and intestinal absorption, reduced toxicity and immune stimulation. The crystal structure of a fully modified MOE-RNA dodecamer duplex (CGCGAAUUCGCG) was determined at 1.7 A resolution. In the majority of the MOE substituents, the torsion angle around the ethylene alkyl chain assumes a gauche conformation. The conformational preorganization of the MOE groups is consistent with the improved RNA affinity and the extensive hydration of the substituents could play a role in the improved cellular uptake of MOE-RNA. A specific hydration pattern that bridges substituent and phosphate oxygen atoms in the minor groove of MOE-RNA may explain its high nuclease resistance.

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Organizational Affiliation: 

Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Medical School, Chicago, Illinois 60611, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*(C43)P*(G48)P*(C43)P*(G48)P*(A44)P*(A44)P*(U36)P*(U36)P*(C43)P*(G48)P*(C43)P*(G48))-3')	A, B	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.258 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.2	α = 90
b = 34.44	β = 92.4
c = 46.62	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-04-29 
• Released Date: 1999-05-12 
Deposition Author(s): Teplova, M., Minasov, G., Tereshko, V., Inamati, G., Cook, P.D., Egli, M.

Revision History  

• Version 1.0: 1999-05-12
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2013-01-16
  Changes: Atomic model
• Version 1.5: 2013-02-27
  Changes: Atomic model