3IBK

Crystal structure of a telomeric RNA quadruplex

Summary for 3IBK

• Entry DOI: 10.2210/pdb3ibk/pdb
• Descriptor: RNA (5'-R(*(5BU)P*AP*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3'), POTASSIUM ION (3 entities in total)
• Functional Keywords: rna quadruplex, bimolecular quadruplex, parallel stranded, rna
• Total number of polymer chains: 2
• Total formula weight: 8054.69

Authors

Collie, G.W.,Neidle, S.,Parkinson, G.N. (deposition date: 2009-07-16, release date: 2010-05-12, Last modification date: 2023-11-01)

Primary citation

Collie, G.W.,Haider, S.M.,Neidle, S.,Parkinson, G.N.
A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex
Nucleic Acids Res., 38:5569-5580, 2010

PubMed Abstract: DNA telomeric repeats in mammalian cells are transcribed to guanine-rich RNA sequences, which adopt parallel-stranded G-quadruplexes with a propeller-like fold. The successful crystallization and structure analysis of a bimolecular human telomeric RNA G-quadruplex, folded into the same crystalline environment as an equivalent DNA oligonucleotide sequence, is reported here. The structural basis of the increased stability of RNA telomeric quadruplexes over DNA ones and their preference for parallel topologies is described here. Our findings suggest that the 2'-OH hydroxyl groups in the RNA quadruplex play a significant role in redefining hydration structure in the grooves and the hydrogen bonding networks. The preference for specific nucleotides to populate the C3'-endo sugar pucker domain is accommodated by alterations in the phosphate backbone, which leads to greater stability through enhanced hydrogen bonding networks. Molecular dynamics simulations on the DNA and RNA quadruplexes are consistent with these findings. The computations, based on the native crystal structure, provide an explanation for RNA G-quadruplex ligand binding selectivity for a group of naphthalene diimide ligands as compared to the DNA G-quadruplex.

PubMed: 20413582
DOI: 10.1093/nar/gkq259

Experimental method

X-RAY DIFFRACTION (2.2 Å)