Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 117, Issue 36, Page 22157-22166, Year 2020
Publish date	Sep 8, 2020
Authors	Ye Zhou / Panagiotis L Kastritis / Shannon E Dougherty / Jonathan Bouvette / Allen L Hsu / Laura Burbaum / Shyamal Mosalaganti / Stefan Pfeffer / Wim J H Hagen / Friedrich Förster / Mario J Borgnia / Christine Vogel / Martin Beck / Alberto Bartesaghi / Gustavo M Silva /
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 ...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.
External links	Proc Natl Acad Sci U S A / PubMed:32855298 / PubMed Central
Methods	EM (tomography) / EM (single particle)
Resolution	2.7 - 4.2 Å
Structure data	EMDB-22190: Subtomogram averaging map of yeast polysome Method: EM (tomography) 22196 6xiq EMDB-22196, PDB-6xiq: Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress Method: EM (single particle) / Resolution: 4.2 Å EMDB-22197: Cryo-EM Structure of K63R Ubiquitin Mutant Consensus Ribosome under Oxidative Stress Method: EM (single particle) / Resolution: 2.7 Å 22198 6xir EMDB-22198, PDB-6xir: Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress Method: EM (single particle) / Resolution: 3.2 Å
Chemicals	ChemComp-ZN: Unknown entry
Source	saccharomyces cerevisiae (brewer's yeast)
Keywords	RIBOSOME / K63 ubiquitin / oxidative stress / translation