7MPI

Stm1 bound vacant 80S structure isolated from cbf5-D95A

This is a non-PDB format compatible entry.

Summary for 7MPI

• Entry DOI: 10.2210/pdb7mpi/pdb
• EMDB information: 23934
• Descriptor: 40S ribosomal protein S0-A, 40S ribosomal protein S9-A, 40S ribosomal protein S10-A, ... (81 entities in total)
• Functional Keywords: yeast, 80s complex, chemical modification, ribosome
• Biological source: Saccharomyces cerevisiae (Baker's yeast); More
• Total number of polymer chains: 79
• Total formula weight: 2940751.60

Authors

Rai, J.,Zhao, Y.,Li, H. (deposition date: 2021-05-04, release date: 2022-05-11, Last modification date: 2022-07-20)

Primary citation

Zhao, Y.,Rai, J.,Yu, H.,Li, H.
CryoEM structures of pseudouridine-free ribosome suggest impacts of chemical modifications on ribosome conformations.
Structure, 30:983-, 2022

PubMed Abstract: Pseudouridine, the most abundant form of RNA modification, is known to play important roles in ribosome function. Mutations in human DKC1, the pseudouridine synthase responsible for catalyzing the ribosome RNA modification, cause translation deficiencies and are associated with a complex cancer predisposition. The structural basis for how pseudouridine impacts ribosome function remains uncharacterized. Here, we characterized structures and conformations of a fully modified and a pseudouridine-free ribosome from Saccharomyces cerevisiae in the absence of ligands or when bound with translocation inhibitor cycloheximide by electron cryomicroscopy. In the modified ribosome, the rearranged N1 atom of pseudouridine is observed to stabilize key functional motifs by establishing predominately water-mediated close contacts with the phosphate backbone. The pseudouridine-free ribosome, however, is devoid of such interactions and displays conformations reflective of abnormal inter-subunit movements. The erroneous motions of the pseudouridine-free ribosome may explain its observed deficiencies in translation.

PubMed: 35489333
DOI: 10.1016/j.str.2022.04.002

Experimental method

ELECTRON MICROSCOPY (3.05 Å)