2GRB

Crystal Structure of an RNA Quadruplex Containing Inosine-tetrad

Summary for 2GRB

• Entry DOI: 10.2210/pdb2grb/pdb
• Descriptor: 5'-R(*(U33)P*GP*IP*GP*GP*U)-3', POTASSIUM ION, STRONTIUM ION, ... (4 entities in total)
• Functional Keywords: rna quadruplex, rna
• Total number of polymer chains: 8
• Total formula weight: 15846.49

Authors

Pan, B.,Shi, K.,Sundaralingam, M. (deposition date: 2006-04-24, release date: 2006-11-21, Last modification date: 2024-02-14)

Primary citation

Pan, B.,Shi, K.,Sundaralingam, M.
Crystal structure of an RNA quadruplex containing inosine tetrad: implications for the roles of NH2 group in purine tetrads.
J.Mol.Biol., 363:451-459, 2006

PubMed Abstract: Polyinosinic acid has been known to adopt the four-stranded helical structure but its basic unit, inosine tetrad (I tetrad), has not been determined at the atomic level. Here we report the crystal structure of an RNA quadruplex containing an I tetrad at 1.4 A resolution. The I tetrad has one cyclic hydrogen bond N1...O6 with the bond length of 2.7 A. A water bridge is observed in the minor groove side of the base tetrad. Even though it is sandwiched by guanine tetrads (G tetrads), the I tetrad is buckled towards the 3' side of the tetrad plane, which results from the different interaction strength with K ions on two sides of the tetrad plane. Comparison with both G tetrad and adenine tetrad indicates that lack of NH2 in the C2 position makes the I tetrad prone to buckle for interactions with ligands. Two U*(G-G-G-G) base pentads are observed at the junction of the 5' termini of two quadruplexes. The uridine residue in the base pentad is engaged in two hydrogen bonding interactions (N2(G)-H...O2(U) and O2'(G)-H...O4(U)) and a water-mediated interaction (N3(G) and N3(U)) with the G tetrad. We also discuss the roles of amino group in purine tetrads and the inter-quadruplex interactions in RNA molecules. These quadruplexes may interact with each other by stacking, groove binding and intercalation.

PubMed: 16978642
DOI: 10.1016/j.jmb.2006.08.022

Experimental method

X-RAY DIFFRACTION (1.4 Å)