PDBsum entry 2adt

RNA

PDB id: 2adt

Contents

DNA/RNA

References listed in PDB file

Key reference

Title

Rna helical packing in solution: nmr structure of a 30 kda gaaa tetraloop-Receptor complex.

Authors

J.H.Davis, M.Tonelli, L.G.Scott, L.Jaeger, J.R.Williamson, S.E.Butcher.

Ref.

J Mol Biol, 2005, 351, 371-382. [DOI no: 10.1016/j.jmb.2005.05.069]

PubMed id

16002091

Abstract

Tertiary interactions are critical for proper RNA folding and ribozyme catalysis. RNA tertiary structure is often condensed through long-range helical packing interactions mediated by loop-receptor motifs. RNA structures displaying helical packing by loop-receptor interactions have been solved by X-ray crystallography, but not by NMR. Here, we report the NMR structure of a 30 kDa GAAA tetraloop-receptor RNA complex. In order to stabilize the complex, we used a modular design in which the RNA was engineered to form a homodimer, with each subunit containing a GAAA tetraloop phased one helical turn apart from its cognate 11-nucleotide receptor domain. The structure determination utilized specific isotopic labeling patterns (2H, 13C and 15N) and refinement against residual dipolar couplings. We observe a unique and highly unusual chemical shift pattern for an adenosine platform interaction that reveals a spectroscopic fingerprint for this motif. The structure of the GAAA tetraloop-receptor interaction is well defined solely from experimental NMR data, shows minor deviations from previously solved crystal structures, and verifies the previously inferred hydrogen bonding patterns within this motif. This work demonstrates the feasibility of using engineered homodimers as modular systems for the determination of RNA tertiary interactions by NMR.

Figure 8.
Figure 8. Structure of the GAAA tetraloop-receptor RNA. The ensemble of the 20 lowest energy structures with one half of the homodimer in red/gold and the other in blue/cyan.

Figure 9.
Figure 9. Comparison of the NMR structure and crystal structure. (a) The ensemble of the 20 lowest energy NMR structures is shown in color, superimposed with the crystal structure (shown in gray). (b) and (c) Base-pairing interactions between the tetraloop and receptor. Hydrogen bonds are indicated with broken lines. Residues from the tetraloop are shown in orange and residues from the receptor are shown in cyan. The crystal structure is in white. G8 is in a Watson-Crick pair with C35 and forms a base quadruplet with A23 and G20 from the tetraloop. A6 is in a reverse-Hoogsteen pair with U36, and forms a triplet with A21 from the tetraloop.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 351, 371-382) copyright 2005.