2XEB

NMR STRUCTURE OF THE PROTEIN-UNBOUND SPLICEOSOMAL U4 SNRNA 5' STEM LOOP

Replaces:  2KR8

Summary for 2XEB

• Entry DOI: 10.2210/pdb2xeb/pdb
• Descriptor: 5'-R(P*GP*AP*UP*CP*GP*UP*AP*GP*CP*CP*AP*AP*UP*GP*AP* GP*GP*UP*U)-3', 5'-R(P*GP*CP*CP*GP*AP*GP*GP*CP*GP*CP*GP*AP*UP*C)-3' (2 entities in total)
• Functional Keywords: rna, pre-mrna splicing, u4/u6 di-snrnp, rnp-binding domain, sans
• Biological source: HOMO SAPIENS (HUMAN); More
• Total number of polymer chains: 2
• Total formula weight: 10635.45

Authors

Falb, M.,Amata, I.,Gabel, F.,Simon, B.,Carlomagno, T. (deposition date: 2010-05-12, release date: 2010-05-26, Last modification date: 2024-05-15)

Primary citation

Falb, M.,Amata, I.,Gabel, F.,Simon, B.,Carlomagno, T.
Structure of the K-turn U4 RNA: a combined NMR and SANS study.
Nucleic Acids Res., 38:6274-6285, 2010

PubMed Abstract: K-turn motifs are universal RNA structural elements providing a binding platform for proteins in several cellular contexts. Their characteristic is a sharp kink in the phosphate backbone that puts the two helical stems of the protein-bound RNA at an angle of 60°. However, to date no high-resolution structure of a naked K-turn motif is available. Here, we present the first structural investigation at atomic resolution of an unbound K-turn RNA (the spliceosomal U4-Kt RNA) by a combination of NMR and small-angle neutron scattering data. With this study, we wish to address the question whether the K-turn structural motif assumes the sharply kinked conformation in the absence of protein binders and divalent cations. Previous studies have addressed this question by fluorescence resonance energy transfer, biochemical assays and molecular dynamics simulations, suggesting that the K-turn RNAs exist in equilibrium between a kinked conformation, which is competent for protein binding, and a more extended conformation, with the population distribution depending on the concentration of divalent cations. Our data shows that the U4-Kt RNA predominantly assumes the more extended conformation in the absence of proteins and divalent cations. The internal loop region is well structured but adopts a different conformation from the one observed in complex with proteins. Our data suggests that the K-turn consensus sequence does not per se code for the kinked conformation; instead the sharp backbone kink requires to be stabilized by protein binders.

PubMed: 20466811
DOI: 10.1093/nar/gkq380

Experimental method

SOLUTION NMR