6HYK

NMR solution structure of the C/D box snoRNA U14

Summary for 6HYK

• Entry DOI: 10.2210/pdb6hyk/pdb
• NMR Information: BMRB: 34321
• Descriptor: RNA (31-MER) (1 entity in total)
• Functional Keywords: snorna, u14, k-turn, snu13p, rna
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 9998.95

Authors

Chagot, M.E.,Quinternet, M.,Rothe, B.,Charpentier, B.,Coutant, J.,Manival, X.,Lebars, I. (deposition date: 2018-10-22, release date: 2019-04-24, Last modification date: 2024-06-19)

Primary citation

Chagot, M.E.,Quinternet, M.,Rothe, B.,Charpentier, B.,Coutant, J.,Manival, X.,Lebars, I.
The yeast C/D box snoRNA U14 adopts a "weak" K-turn like conformation recognized by the Snu13 core protein in solution.
Biochimie, 164:70-82, 2019

PubMed Abstract: Non-coding RNAs associate with proteins to form ribonucleoproteins (RNPs), such as ribosome, box C/D snoRNPs, H/ACA snoRNPs, ribonuclease P, telomerase and spliceosome to ensure cell viability. The assembly of these RNA-protein complexes relies on the ability of the RNA to adopt the correct bound conformation. K-turn motifs represent ubiquitous binding platform for proteins found in several cellular environment. This structural motif has an internal three-nucleotide bulge flanked on its 3' side by a G•A/A•G tandem pairs followed by one or two non-Watson-Crick pairs, and on its 5' side by a classical RNA helix. This peculiar arrangement induces a strong curvature of the phosphodiester backbone, which makes it conducive to multiple tertiary interactions. SNU13/Snu13p (Human/Yeast) binds specifically the U14 C/D box snoRNA K-turn sequence motif. This event is the prerequisite to promote the assembly of the RNP, which contains NOP58/Nop58 and NOP56/Nop56 core proteins and the 2'-O-methyl-transferase, Fibrillarin/Nop1p. The U14 small nucleolar RNA is a conserved non-coding RNA found in yeast and vertebrates required for the pre-rRNA maturation and ribose methylation. Here, we report the solution structure of the free U14 snoRNA K-turn motif (kt-U14) as determined by Nuclear Magnetic Resonance. We demonstrate that a major fraction of free kt-U14 adopts a pre-folded conformation similar to protein bound K-turn, even in the absence of divalent ions. In contrast to the kt-U4 or tyrS RNA, kt-U14 displays a sharp bent in the phosphodiester backbone. The U•U and G•A tandem base pairs are formed through weak hydrogen bonds. Finally, we show that the structure of kt-U14 is stabilized upon Snu13p binding. The structure of the free U14 RNA is the first reference example for the canonical motifs of the C/D box snoRNA family.

PubMed: 30914254
DOI: 10.1016/j.biochi.2019.03.014

Experimental method

SOLUTION NMR