6XIR

Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress

This is a non-PDB format compatible entry.

Summary for 6XIR

• Entry DOI: 10.2210/pdb6xir/pdb
• EMDB information: 22190 22196 22197 22198
• Descriptor: 60S ribosomal protein L2-A, RPL11B isoform 1, 60S ribosomal protein L13-A, ... (76 entities in total)
• Functional Keywords: k63 ubiquitin, ribosome, oxidative stress, translation
• Biological source: Saccharomyces cerevisiae (Baker's yeast); More
• Total number of polymer chains: 76
• Total formula weight: 3100566.79

Authors

Zhou, Y.,Bartesaghi, A.,Silva, G.M. (deposition date: 2020-06-21, release date: 2020-08-26, Last modification date: 2024-10-23)

Primary citation

Zhou, Y.,Kastritis, P.L.,Dougherty, S.E.,Bouvette, J.,Hsu, A.L.,Burbaum, L.,Mosalaganti, S.,Pfeffer, S.,Hagen, W.J.H.,Forster, F.,Borgnia, M.J.,Vogel, C.,Beck, M.,Bartesaghi, A.,Silva, G.M.
Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress.
Proc.Natl.Acad.Sci.USA, 117:22157-22166, 2020

PubMed 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.

PubMed: 32855298
DOI: 10.1073/pnas.2005301117

Experimental method

ELECTRON MICROSCOPY (3.2 Å)