8PV8

Chaetomium thermophilum pre-60S State 4 - post-5S rotation with Rix1 complex without Foot - composite structure

This is a non-PDB format compatible entry.

Summary for 8PV8

• Entry DOI: 10.2210/pdb8pv8/pdb
• EMDB information: 17899 17900 17901 17902 17957
• Descriptor: 26S rRNA, Zinc finger domain-containing protein, Nucleolar GTP-binding protein 2, ... (62 entities in total)
• Functional Keywords: biogenesis, pre-60s, 5s rnp, ribosome
• Biological source: Thermochaetoides thermophila DSM 1495; More
• Total number of polymer chains: 60
• Total formula weight: 3121375.96

Authors

Thoms, M.,Cheng, J.,Denk, T.,Berninghausen, O.,Beckmann, R. (deposition date: 2023-07-17, release date: 2024-01-10, Last modification date: 2024-01-17)

Primary citation

Thoms, M.,Lau, B.,Cheng, J.,Fromm, L.,Denk, T.,Kellner, N.,Flemming, D.,Fischer, P.,Falquet, L.,Berninghausen, O.,Beckmann, R.,Hurt, E.
Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
Embo Rep., 24:e57984-e57984, 2023

PubMed 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.

PubMed: 37921038
DOI: 10.15252/embr.202357984

Experimental method

ELECTRON MICROSCOPY (2.91 Å)