246D

STRUCTURE OF THE PURINE-PYRIMIDINE ALTERNATING RNA DOUBLE HELIX, R(GUAUAUA)D(C) , WITH A 3'-TERMINAL DEOXY RESIDUE

Summary for 246D

• Entry DOI: 10.2210/pdb246d/pdb
• Descriptor: DNA/RNA (5'-R(*GP*UP*AP*UP*AP*UP*AP*)-D(*C)-3'), SODIUM ION (3 entities in total)
• Functional Keywords: a-dna/rna, double helix, dna-rna complex, dna/rna
• Total number of polymer chains: 2
• Total formula weight: 5037.07

Authors

Wahl, M.C.,Ban, C.,Sekharudu, C.,Ramakrishnan, B.,Sundaralingam, M. (deposition date: 1996-01-25, release date: 1996-08-26, Last modification date: 2024-02-14)

Primary citation

Wahl, M.C.,Ban, C.,Sekharudu, C.,Ramakrishnan, B.,Sundaralingam, M.
Structure of the purine-pyrimidine alternating RNA double helix, r(GUAUAUA)d(C), with a 3'-terminal deoxy residue.
Acta Crystallogr.,Sect.D, 52:655-667, 1996

PubMed Abstract: The crystal structure of the purine-pyrimidine alternating octameric RNA helix, r(GUAUAUA)d(C), carrying a 3'-terminal deoxycytidine residue, has been determined at 2.2 A resolution. The molecule crystallizes in the rhombohedral space group R3 (hexagonal cell constants: a = b = 43.07,c = 59.36 A;alpha = beta = 90,gamma = 120 degrees )with one duplex in an asymmetric unit. The structure was solved by molecular replacement and refined with 83 and 2/3 solvent molecules and 2/3 sodium ions to a final R factor of 15.6% using 1775 reflections (86%). The duplexes are approximately linear, their global helix axes are inclined by 10 degrees with respect to the 3(2)-screw axes, and they are stacked on top of each other in a head-to-tail fashion. The twist between the junction base pairs of the stacked duplexes is negligible resulting in a discontinuity of the helix backbones and grooves. The sodium ions on the threefold axis play a significant role in the organization of the packing network. The helical parameters, particularly the twist and the roll, of this alternating sequence are in accord with Calladine's rules. Almost all the 2'-hydroxyl groups are involved in specific hydrogen-bonding interactions, either directly to the sugar ring oxygens O4' on the 3' side, or, through water bridges, to the sugars, phosphates, or bases. This hydrogen bonding of the 2'-hydroxyl groups restrains the conformation of the sugar-phosphate backbone and the glycosidic torsion angles of this RNA fragment. The lack of intermolecular packing contacts in the grooves provides a clear picture of the groove solvation.

PubMed: 15299629
DOI: 10.1107/S0907444996000248

Experimental method

X-RAY DIFFRACTION (2.2 Å)