1RNA | pdb_00001rna

CRYSTALLOGRAPHIC STRUCTURE OF AN RNA HELIX: [U(U-A)6A]2

• PDB DOI: https://doi.org/10.2210/pdb1RNA/pdb
• NAKB: 1RNA

• Classification: RNA
• Mutation(s): No 


• Deposited: 1990-02-01 Released: 1991-04-15 
• Deposition Author(s): Dock-Bregeon, A.C., Chevrier, B., Podjarny, A., Johnson, J., De Bear, J.S., Gough, G.R., Gilham, P.T., Moras, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Observed: 
  0.131 (Depositor) 

Literature

Crystallographic structure of an RNA helix: [U(UA)6A]2.

Dock-Bregeon, A.C., Chevrier, B., Podjarny, A., Johnson, J., de Bear, J.S., Gough, G.R., Gilham, P.T., Moras, D.

(1989) J Mol Biology 209: 459-474

• PubMed: 2479753 
• DOI: https://doi.org/10.1016/0022-2836(89)90010-7
• Primary Citation Related Structures: 
  1RNA


• PubMed Abstract: 
  

  The crystallographic structure of the synthetic oligoribonucleotide, U(UA)6A, has been solved at 2.25 A resolution. The crystallographic refinement permitted the identification of 91 solvent molecules, with a final agreement factor of 13%. The molecule is a dimer of 14 base-pairs and shows the typical features of an A-type helix. However, the presence of two kinks causes a divergence from a straight helix. The observed deformation, which is stabilized by a few hydrogen bonds in the crystal packing, could be due to the relatively high (35 degrees C) temperature of crystallization. The complete analysis of the structure is presented. It includes the stacking geometries, the backbone conformation and the solvation.

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Organizational Affiliation: 
• Institut de Biologie Moléculaire et Cellulaire de C.N.R.S., Strasbourg, France.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.81 kDa 
• Atom Count: 673 
• Modeled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*UP*AP*A)-3')	A, B	14	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Observed: 0.131 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.11	α = 90
b = 44.61	β = 90
c = 49.11	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1991-04-15 
Deposition Author(s): Dock-Bregeon, A.C., Chevrier, B., Podjarny, A., Johnson, J., De Bear, J.S., Gough, G.R., Gilham, P.T., Moras, D.

Revision History  

• Version 1.0: 1991-04-15
  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: 2018-04-18
  Changes: Data collection
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references