SNAP output for PDB entry 6wpi [SNAP web server]

PDB-id

6wpi; SNAP-derived features in text and JSON formats; DNAproDB

Class

RNA binding protein-RNA

Method

X-ray (3.02 Å)

Summary

Crystal structure of nop9 in complex with its1 RNA

Reference

Zhang J, Teramoto T, Qiu C, Wine RN, Gonzalez LE, Baserga SJ, Tanaka Hall TM (2020): "Nop9 recognizes structured and single-stranded RNA elements of preribosomal RNA." Rna, 26, 1049-1059. doi: 10.1261/rna.075416.120.

Abstract

Nop9 is an essential factor in the processing of pre-ribosomal RNA. Its absence in yeast is lethal, and defects in the human ortholog are associated with breast cancer, autoimmunity, and learning/language impairment. PUF family RNA-binding proteins are best known for sequence-specific RNA recognition, and most contain eight α-helical repeats that bind to the RNA bases of single-stranded RNA. Nop9 is an unusual member of this family in that it contains eleven repeats and recognizes both RNA structure and sequence. Here we report a crystal structure of Saccharomyces cerevisiae Nop9 in complex with its target RNA within the 20S pre-ribosomal RNA. This structure reveals that Nop9 brings together a C-terminal module recognizing the 5' single-stranded region of the RNA and a bifunctional N-terminal module recognizing the central double-stranded stem region. We further show that the 3' single-stranded region of the 20S target RNA adds sequence-independent binding energy to the RNA-Nop9 interaction. Both the N- and C-terminal modules retain the characteristic sequence-specific recognition of PUF proteins but the N-terminal module has also evolved a distinct interface, which allows Nop9 to recognize either single-stranded RNA sequences or RNAs with a combination of single-stranded and structured elements.