EMD-23806

Single-particle
3.35 Å
EMD-23806 Deposition: 08/04/2021
Map released: 24/11/2021
Last modified: 29/05/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-23806

Structure of yeast Ubr1 in complex with Ubc2 and N-degron

EMD-23806

Single-particle
3.35 Å
EMD-23806 Deposition: 08/04/2021
Map released: 24/11/2021
Last modified: 29/05/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Homo sapiens
Sample: yeast Ubr1 in complex with Ubc2 and N-degron
Fitted models: 7mex (Avg. Q-score: 0.45)
Raw data: EMPIAR-10886

Deposition Authors: Pan M , Zheng Q
Structural insights into Ubr1-mediated N-degron polyubiquitination.
Pan M , Zheng Q, Wang T , Liang L, Mao J, Zuo C , Ding R , Ai H, Xie Y , Si D , Yu Y , Liu L , Zhao M
(2021) Nature , 600 , 334 - 338
PUBMED: 34789879
DOI: doi:10.1038/s41586-021-04097-8
ISSN: 1476-4687
ASTM: NATUAS
Abstract:
The N-degron pathway targets proteins that bear a destabilizing residue at the N terminus for proteasome-dependent degradation1. In yeast, Ubr1-a single-subunit E3 ligase-is responsible for the Arg/N-degron pathway2. How Ubr1 mediates the initiation of ubiquitination and the elongation of the ubiquitin chain in a linkage-specific manner through a single E2 ubiquitin-conjugating enzyme (Ubc2) remains unknown. Here we developed chemical strategies to mimic the reaction intermediates of the first and second ubiquitin transfer steps, and determined the cryo-electron microscopy structures of Ubr1 in complex with Ubc2, ubiquitin and two N-degron peptides, representing the initiation and elongation steps of ubiquitination. Key structural elements, including a Ubc2-binding region and an acceptor ubiquitin-binding loop on Ubr1, were identified and characterized. These structures provide mechanistic insights into the initiation and elongation of ubiquitination catalysed by Ubr1.