EMD-26703

Single-particle
2.44 Å
EMD-26703 Deposition: 20/04/2022
Map released: 15/03/2023
Last modified: 12/06/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-26703

Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1 D52A strain

EMD-26703

Single-particle
2.44 Å
EMD-26703 Deposition: 20/04/2022
Map released: 15/03/2023
Last modified: 12/06/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Saccharomyces cerevisiae BY4741
Sample: Nucleolar 60S intermediate purified with tags on Tif6 and Nog2 from a SPB1 D52A strain
Fitted models: 7uqz (Avg. Q-score: 0.608)

Deposition Authors: Sekulski K , Cruz VE , Weirich CS , Erzberger JP
rRNA methylation by Spb1 regulates the GTPase activity of Nog2 during 60S ribosomal subunit assembly.
Sekulski K , Cruz VE , Weirich CS , Erzberger JP
(2023) Nat Commun , 14 , 1207 - 1207
PUBMED: 36864048
DOI: doi:10.1038/s41467-023-36867-5
ISSN: 2041-1723
Abstract:
Biogenesis of the large ribosomal (60S) subunit involves the assembly of three rRNAs and 46 proteins, a process requiring approximately 70 ribosome biogenesis factors (RBFs) that bind and release the pre-60S at specific steps along the assembly pathway. The methyltransferase Spb1 and the K-loop GTPase Nog2 are essential RBFs that engage the rRNA A-loop during sequential steps in 60S maturation. Spb1 methylates the A-loop nucleotide G2922 and a catalytically deficient mutant strain (spb1D52A) has a severe 60S biogenesis defect. However, the assembly function of this modification is currently unknown. Here, we present cryo-EM reconstructions that reveal that unmethylated G2922 leads to the premature activation of Nog2 GTPase activity and capture a Nog2-GDP-AlF4- transition state structure that implicates the direct involvement of unmodified G2922 in Nog2 GTPase activation. Genetic suppressors and in vivo imaging indicate that premature GTP hydrolysis prevents the efficient binding of Nog2 to early nucleoplasmic 60S intermediates. We propose that G2922 methylation levels regulate Nog2 recruitment to the pre-60S near the nucleolar/nucleoplasmic phase boundary, forming a kinetic checkpoint to regulate 60S production. Our approach and findings provide a template to study the GTPase cycles and regulatory factor interactions of the other K-loop GTPases involved in ribosome assembly.