PDBsum entry 1kd4

RNA

PDB id: 1kd4

Contents

DNA/RNA

Metals

_BA ×2

Waters ×69

PDB id:

1kd4

Name:

RNA

Title:

The crystal structure of r(ggucacagccc)2, barium form

Structure:

5'-r( Gp Gp Up Cp Ap Cp Ap Gp Cp Cp C)-3'. Chain: a, b. Engineered: yes

Source:

Synthetic: yes

Biol. unit:

Dimer (from PQS)

Resolution:

1.85Å R-factor: 0.203 R-free: 0.222

Authors:

V.Kacer,S.A.Scaringe,J.N.Scarsdale,J.P.Rife

Key ref:

V.Kacer et al. (2003). Crystal structures of r(GGUCACAGCCC)2. Acta Crystallogr D Biol Crystallogr, 59, 423-432. PubMed id: 12595698 DOI: 10.1107/S0907444902021911

Date:

12-Nov-01 Release date: 04-Mar-03

DNA/RNA chains

G-G-U-C-A-C-A-G-C-C-C 11 bases

G-G-U-C-A-C-A-G-C-C-C 11 bases

DOI no: 10.1107/S0907444902021911

Acta Crystallogr D Biol Crystallogr 59:423-432 (2003)

PubMed id: 12595698

Crystal structures of r(GGUCACAGCCC)2.

V.Kacer, S.A.Scaringe, J.N.Scarsdale, J.P.Rife.

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.

Selected figure(s)

Figure 1.
Figure 1 (a) Sequence of the heterodimer vkIX with strands A and B. (b) Sequence of the homodimer vkIX-AA composed of strand A only.

Figure 5.
Figure 5 Metal coordination to vkIX-AA. Coordination bonds are shown in blue and waters are shown as red spheres. (a) The two Tl atoms (magenta) coordinated to vkIX-AA. (b) Detail of one of the two Tl+ sites. Tl+ coordinates to N7 of A7, O2 and N3 of C4, O4 of U3 and three water molecule O atoms. (c) The two Ba atoms (magenta) coordinated to vkIX-AA. (d) Detail of one of the two Ba^2+ sites. Ba^2+ coordinates to O6 of G8, O4 of U3, O6 of G2 and six water molecule O atoms. The image was created using the program RIBBONS (Carson, 1991[128] [Carson, M. (1991). J. Appl. Cryst. 24, 958-961.]-[129][bluearr.gif] ) and rendered using the program POV-Ray ([130]http://www.povray.org ).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2003, 59, 423-432) copyright 2003.

Figures were selected by the author.