8CBJ

Cryo-EM structure of Otu2-bound cytoplasmic pre-40S ribosome biogenesis complex

This is a non-PDB format compatible entry.

Summary for 8CBJ

• Entry DOI: 10.2210/pdb8cbj/pdb
• Related: 8C83 8CAH 8CAS
• EMDB information: 16470 16471 16525 16533 16541
• Descriptor: 40S ribosomal protein S27-A, non-specific serine/threonine protein kinase, 40S ribosomal protein S0-A, ... (41 entities in total)
• Functional Keywords: ribosome, translation, ubiquitin, deubiquitinating enzyme, biogenesis, complex
• Biological source: Saccharomyces cerevisiae W303; More
• Total number of polymer chains: 39
• Total formula weight: 1604177.94

Authors

Ikeuchi, K.,Buschauer, R.,Cheng, J.,Berninghausen, O.,Becker, T.,Beckmann, R. (deposition date: 2023-01-25, release date: 2023-05-24, Last modification date: 2024-07-24)

Primary citation

Ikeuchi, K.,Ivic, N.,Buschauer, R.,Cheng, J.,Frohlich, T.,Matsuo, Y.,Berninghausen, O.,Inada, T.,Becker, T.,Beckmann, R.
Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2.
Nat Commun, 14:2730-2730, 2023

PubMed Abstract: In actively translating 80S ribosomes the ribosomal protein eS7 of the 40S subunit is monoubiquitinated by the E3 ligase Not4 and deubiquitinated by Otu2 upon ribosomal subunit recycling. Despite its importance for translation efficiency the exact role and structural basis for this translational reset is poorly understood. Here, structural analysis by cryo-electron microscopy of native and reconstituted Otu2-bound ribosomal complexes reveals that Otu2 engages 40S subunits mainly between ribosome recycling and initiation stages. Otu2 binds to several sites on the intersubunit surface of the 40S that are not occupied by any other 40S-binding factors. This binding mode explains the discrimination against 80S ribosomes via the largely helical N-terminal domain of Otu2 as well as the specificity for mono-ubiquitinated eS7 on 40S. Collectively, this study reveals mechanistic insights into the Otu2-driven deubiquitination steps for translational reset during ribosome recycling/(re)initiation.

PubMed: 37169754
DOI: 10.1038/s41467-023-38161-w

Experimental method

ELECTRON MICROSCOPY (3.8 Å)