7QDD

NMR structure of Npl3 RRM1 bound to the AUCCAA RNA

Summary for 7QDD

• Entry DOI: 10.2210/pdb7qdd/pdb
• NMR Information: BMRB: 34691
• Descriptor: RNA (5'-R(*AP*UP*CP*CP*AP*A)-3'), Nucleolar protein 3 (2 entities in total)
• Functional Keywords: splicing, u2 snrna, rrm, split-icrac, yeast, protein-rna complex, rna binding protein
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); More
• Total number of polymer chains: 2
• Total formula weight: 11980.67

Authors

Clery, A.,Allain, F.H.-T.,Moursy, A. (deposition date: 2021-11-26, release date: 2022-10-26, Last modification date: 2024-01-10)

Primary citation

Moursy, A.,Clery, A.,Gerhardy, S.,Betz, K.M.,Rao, S.,Mazur, J.,Campagne, S.,Beusch, I.,Duszczyk, M.M.,Robinson, M.D.,Panse, V.G.,Allain, F.H.
RNA recognition by Npl3p reveals U2 snRNA-binding compatible with a chaperone role during splicing.
Nat Commun, 14:7166-7166, 2023

PubMed Abstract: The conserved SR-like protein Npl3 promotes splicing of diverse pre-mRNAs. However, the RNA sequence(s) recognized by the RNA Recognition Motifs (RRM1 & RRM2) of Npl3 during the splicing reaction remain elusive. Here, we developed a split-iCRAC approach in yeast to uncover the consensus sequence bound to each RRM. High-resolution NMR structures show that RRM2 recognizes a 5´-GNGG-3´ motif leading to an unusual mille-feuille topology. These structures also reveal how RRM1 preferentially interacts with a CC-dinucleotide upstream of this motif, and how the inter-RRM linker and the region C-terminal to RRM2 contribute to cooperative RNA-binding. Structure-guided functional studies show that Npl3 genetically interacts with U2 snRNP specific factors and we provide evidence that Npl3 melts U2 snRNA stem-loop I, a prerequisite for U2/U6 duplex formation within the catalytic center of the B spliceosomal complex. Thus, our findings suggest an unanticipated RNA chaperoning role for Npl3 during spliceosome active site formation.

PubMed: 37935663
DOI: 10.1038/s41467-023-42962-4

Experimental method

SOLUTION NMR