EMD-22197

Single-particle
2.7 Å
EMD-22197 Deposition: 21/06/2020
Map released: 26/08/2020
Last modified: 10/03/2021
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-22197

Cryo-EM Structure of K63R Ubiquitin Mutant Consensus Ribosome under Oxidative Stress

EMD-22197

Single-particle
2.7 Å
EMD-22197 Deposition: 21/06/2020
Map released: 26/08/2020
Last modified: 10/03/2021
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Saccharomyces cerevisiae
Sample: K63 ubiquitinated Ribosome

Deposition Authors: Zhou Y, Bartesaghi A, Silva GM
Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress.
PUBMED: 32855298
DOI: doi:10.1073/pnas.2005301117
ISSN: 1091-6490
ASTM: PNASA6
Abstract:
Subpopulations of ribosomes are responsible for fine tuning the control of protein synthesis in dynamic environments. K63 ubiquitination of ribosomes has emerged as a new posttranslational modification that regulates protein synthesis during cellular response to oxidative stress. K63 ubiquitin, a type of ubiquitin chain that functions independently of the proteasome, modifies several sites at the surface of the ribosome, however, we lack a molecular understanding on how this modification affects ribosome structure and function. Using cryoelectron microscopy (cryo-EM), we resolved the first three-dimensional (3D) structures of K63 ubiquitinated ribosomes from oxidatively stressed yeast cells at 3.5-3.2 Å resolution. We found that K63 ubiquitinated ribosomes are also present in a polysome arrangement, similar to that observed in yeast polysomes, which we determined using cryoelectron tomography (cryo-ET). We further showed that K63 ubiquitinated ribosomes are captured uniquely at the rotated pretranslocation stage of translation elongation. In contrast, cryo-EM structures of ribosomes from mutant cells lacking K63 ubiquitin resolved at 4.4-2.7 Å showed 80S ribosomes represented in multiple states of translation, suggesting that K63 ubiquitin regulates protein synthesis at a selective stage of elongation. Among the observed structural changes, ubiquitin mediates the destabilization of proteins in the 60S P-stalk and in the 40S beak, two binding regions of the eukaryotic elongation factor eEF2. These changes would impact eEF2 function, thus, inhibiting translocation. Our findings help uncover the molecular effects of K63 ubiquitination on ribosomes, providing a model of translation control during oxidative stress, which supports elongation halt at pretranslocation.