Summary information and primary citation

PDB-id
1kd5; DSSR-derived features in text and JSON formats
Class
RNA
Method
X-ray (1.58 Å)
Summary
The crystal structure of r(ggucacagccc)2 metal free form
Reference
Kacer V, Scaringe SA, Scarsdale JN, Rife JP (2003): "Crystal structures of r(GGUCACAGCCC)2." Acta Crystallogr.,Sect.D, 59, 423-432. doi: 10.1107/S0907444902021911.
Abstract
Crystals of small RNAs, which regularly diffract to very high resolution, can often be readily obtained. Unfortunately, for some RNAs the conformations adopted in the crystalline form are different from those found in solution. For example, short RNAs that form hairpins in solution virtually never crystallize thus; rather, they form duplexes. Nevertheless, these unintended structures have contributed greatly to the understanding of RNA structure. In a similar occurrence, the homodimer r(GGUCACAGCCC)(2) has been crystallized from an 11-mer/12-mer heteroduplex, r(GGCUGAAGUCCG)/r(GGUCACAGCCC). This surprising phenomenon was observed under a variety of crystallization conditions. The structure of the homoduplex was determined from crystals that differed in the precipitant used and the type of metal present. In all cases, the resulting homoduplexes contain ten base pairings, of which the central six are non-canonical pairings. In two of the variants, ordered metal-binding sites were observed: two equivalent octacoordinate Tl(+) sites in one and two equivalent nanocoordinate Ba(2+) sites in another.

Cartoon-block schematics in six views (download the tarball)

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