DSSR-PyMOL cartoon-block schematics: PDB entry 3d0m

PDB-id

3d0m; DSSR-derived features in text and JSON formats

Class

RNA

Method

X-ray (2.0 Å)

Summary

X-ray structures of the (guggucugaugaggcc) RNA duplex

Reference

Rypniewski W, Adamiak DA, Milecki J, Adamiak RW (2008): "Noncanonical G(syn)-G(anti) base pairs stabilized by sulphate anions in two X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex." Rna, 14, 1845-1851. doi: 10.1261/rna.1164308.

Abstract

The structures of two crystal forms of the RNA 16-mer with the sequence GUGGUCUGAUGAGGCC, grown in the presence of a high concentration of sulphate ions, have been determined using synchrotron radiation at 1.4- and 2.0-A resolution. RNA with this sequence is known as one of the two strands of the noncleavable form of the hammerhead ribozyme. In both crystal structures, two G(syn)-G(anti) noncanonical base pairs are observed in the middle of a 14 base-pair (bp) duplex having 5'-dangling GU residues. Both structures contain sulphate anions interacting with the G-G bp stabilizing G in its syn conformation and bridging the two RNA strands. In both cases the interactions take place in the major groove, although the anions are accommodated within different helix geometries, most pronounced in the changing width of the major groove. In one structure, where a single sulphate spans both G-G pairs, the major groove is closed around the anion, while in the other structure, where each of the two G-G pairs is associated with a separate sulphate, the groove is open. This work provides the first examples of a G-G pair in syn-anti conformation, which minimizes the purine-purine clash in the center of the duplex, while utilizing its residual hydrogen bonding potential in specific interactions with sulphate anions.