EMD-17956

Single-particle
2.12 Å
EMD-17956 Deposition: 17/07/2023
Map released: 15/11/2023
Last modified: 20/12/2023
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-17956

Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - Composite structure

EMD-17956

Single-particle
2.12 Å
EMD-17956 Deposition: 17/07/2023
Map released: 15/11/2023
Last modified: 20/12/2023
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Thermochaetoides thermophila DSM 1495
Sample: Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - Composite structure
Fitted models: 8pv7 (Avg. Q-score: 0.676)

Deposition Authors: Thoms M , Cheng J , Denk T , Berninghausen O, Beckmann R
Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
Thoms M , Lau B , Cheng J , Fromm L , Denk T , Kellner N, Flemming D , Fischer P, Falquet L , Berninghausen O, Beckmann R , Hurt E
(2023) EMBO Rep , 24 , e57984 - e57984
PUBMED: 37921038
DOI: doi:10.15252/embr.202357984
ISSN: 1469-3178
Abstract:
The rixosome defined in Schizosaccharomyces pombe and humans performs diverse roles in pre-ribosomal RNA processing and gene silencing. Here, we isolate and describe the conserved rixosome from Chaetomium thermophilum, which consists of two sub-modules, the sphere-like Rix1-Ipi3-Ipi1 and the butterfly-like Las1-Grc3 complex, connected by a flexible linker. The Rix1 complex of the rixosome utilizes Sda1 as landing platform on nucleoplasmic pre-60S particles to wedge between the 5S rRNA tip and L1-stalk, thereby facilitating the 180° rotation of the immature 5S RNP towards its mature conformation. Upon rixosome positioning, the other sub-module with Las1 endonuclease and Grc3 polynucleotide-kinase can reach a strategic position at the pre-60S foot to cleave and 5' phosphorylate the nearby ITS2 pre-rRNA. Finally, inward movement of the L1 stalk permits the flexible Nop53 N-terminus with its AIM motif to become positioned at the base of the L1-stalk to facilitate Mtr4 helicase-exosome participation for completing ITS2 removal. Thus, the rixosome structure elucidates the coordination of two central ribosome biogenesis events, but its role in gene silencing may adapt similar strategies.