1KD4

The Crystal Structure of r(GGUCACAGCCC)2, Barium form

Summary for 1KD4

• Entry DOI: 10.2210/pdb1kd4/pdb
• Descriptor: 5'-R(*GP*GP*UP*CP*AP*CP*AP*GP*CP*CP*C)-3', BARIUM ION (3 entities in total)
• Functional Keywords: rna duplex, metal binding, rna
• Total number of polymer chains: 2
• Total formula weight: 7236.95

Authors

Kacer, V.,Scaringe, S.A.,Scarsdale, J.N.,Rife, J.P. (deposition date: 2001-11-12, release date: 2003-03-04, Last modification date: 2024-02-07)

Primary citation

Kacer, V.,Scaringe, S.A.,Scarsdale, J.N.,Rife, J.P.
Crystal structures of r(GGUCACAGCCC)2.
Acta Crystallogr.,Sect.D, 59:423-432, 2003

PubMed 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.

PubMed: 12595698
DOI: 10.1107/S0907444902021911

Experimental method

X-RAY DIFFRACTION (1.85 Å)