5G4T

The structure of a quasi-cyclic six k-turn duplex RNA species

Summary for 5G4T

• Entry DOI: 10.2210/pdb5g4t/pdb
• Descriptor: HMKT-7 (2 entities in total)
• Functional Keywords: rna, kink turn, rna motif, nano-structure, nanotechnology
• Biological source: HALOARCULA MARISMORTUI; More
• Total number of polymer chains: 2
• Total formula weight: 6190.84

Authors

Huang, L.,Lilley, D.M.J. (deposition date: 2016-05-17, release date: 2016-09-28, Last modification date: 2024-01-10)

Primary citation

Huang, L.,Lilley, D.M.J.
A Quasi-Cyclic RNA Nano-Scale Molecular Object Constructed Using Kink Turns.
Nanoscale, 8:15189-, 2016

PubMed Abstract: k-Turns are widespread RNA architectural elements that mediate tertiary interactions. We describe a double-kink-turn motif comprising two inverted k-turns that forms a tight horse-shoe structure that can assemble into a variety of shapes by coaxial association of helical ends. Using X-ray crystallography we show that these assemble with two (dumbell), three (triangle) and four units (square), with or without bound protein, within the crystal lattice. In addition, exchange of a single basepair can almost double the pore radius or shape of a molecular assembly. On the basis of this analysis we synthesized a 114 nt self-complementary RNA containing six k-turns. The crystal structure of this species shows that it forms a quasi-cyclic triangular object. These are randomly disposed about the three-fold axis in the crystal lattice, generating a circular RNA of quasi D3 symmetry with a shape reminiscent of that of a cyclohexane molecule in its chair conformation. This work demonstrates that the k-turn is a powerful building block in the construction of nano-scale molecular objects, and illustrates why k-turns are widely used in natural RNA molecules to organize long-range architecture and mediate tertiary contacts.

PubMed: 27506301
DOI: 10.1039/C6NR05186C

Experimental method

X-RAY DIFFRACTION (2.751 Å)