9GY4

60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF and LTN1 (Composite map)

This is a non-PDB format compatible entry.

Summary for 9GY4

• Entry DOI: 10.2210/pdb9gy4/pdb
• EMDB information: 51681
• Descriptor: 28S rRNA, 60S ribosomal protein L3, 60S ribosomal protein L4, ... (57 entities in total)
• Functional Keywords: 60s, ufmylation, er, rqc, ribosome
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 55
• Total formula weight: 3177890.88

Authors

Penchev, I.,Gumbin, S.,Becker, T.,Kopito, R.,Beckmann, R. (deposition date: 2024-10-01, release date: 2025-05-14)

Primary citation

Penchev, I.,Gumbin, S.,Scavone, F.,Berninghausen, O.,Becker, T.,Kopito, R.,Beckmann, R.
UFMylation orchestrates spatiotemporal coordination of RQC at the ER.
Sci Adv, 11:eadv0435-eadv0435, 2025

PubMed Abstract: Degradation of arrest peptides from endoplasmic reticulum (ER) translocon-bound 60 ribosomal subunits via the ribosome-associated quality control (ER-RQC) pathway requires covalent modification of RPL26/uL24 on 60 ribosomal subunits with UFM1. However, the underlying mechanism that coordinates the UFMylation and RQC pathways remains elusive. Structural analysis of ER-RQC intermediates revealed concomitant binding and direct interaction of the UFMylation and RQC machineries on the 60. In the presence of an arrested peptidyl-transfer RNA, the RQC factor NEMF and the UFM1 E3 ligase (E3) form a direct interaction via the UFL1 subunit of E3, and UFL1 adopts a conformation distinct from that previously observed for posttermination 60. While this concomitant binding occurs on translocon-bound 60, LTN1 recruitment and arrest peptide degradation require UFMylation-dependent 60 dissociation from the translocon. These data reveal a mechanism by which the UFMylation cycle orchestrates ER-RQC.

PubMed: 40315331
DOI: 10.1126/sciadv.adv0435

Experimental method

ELECTRON MICROSCOPY (3 Å)