7BV8

Mature 50S ribosomal subunit from RrmJ knock out E.coli strain

Summary for 7BV8

• Entry DOI: 10.2210/pdb7bv8/pdb
• EMDB information: 30211 30212 30213 30214 30215
• Descriptor: 23S rRNA, 50S ribosomal protein L11, 50S ribosomal protein L13, ... (32 entities in total)
• Functional Keywords: ribosome assembly, ribosome biogenesis, ribosome
• Biological source: Escherichia coli (strain K12); More
• Total number of polymer chains: 32
• Total formula weight: 1374986.36

Authors

Wang, W.,Li, W.Q.,Ge, X.L.,Yan, K.G.,Mandava, C.S.,Sanyal, S.,Gao, N. (deposition date: 2020-04-09, release date: 2020-07-01, Last modification date: 2024-03-27)

Primary citation

Wang, W.,Li, W.,Ge, X.,Yan, K.,Mandava, C.S.,Sanyal, S.,Gao, N.
Loss of a single methylation in 23S rRNA delays 50S assembly at multiple late stages and impairs translation initiation and elongation.
Proc.Natl.Acad.Sci.USA, 117:15609-15619, 2020

PubMed Abstract: Ribosome biogenesis is a complex process, and dozens of factors are required to facilitate and regulate the subunit assembly in bacteria. The 2'-O-methylation of U2552 in 23S rRNA by methyltransferase RrmJ is a crucial step in late-stage assembly of the 50S subunit. Its absence results in severe growth defect and marked accumulation of pre50S assembly intermediates. In the present work, we employed cryoelectron microscopy to characterize a set of late-stage pre50S particles isolated from an Δ strain. These assembly intermediates (solved at 3.2 to 3.8 Å resolution) define a collection of late-stage particles on a progressive assembly pathway. Apart from the absence of L16, L35, and L36, major structural differences between these intermediates and the mature 50S subunit are clustered near the peptidyl transferase center, such as H38, H68-71, and H89-93. In addition, the ribosomal A-loop of the mature 50S subunit from Δ strain displays large local flexibility on nucleotides next to unmethylated U2552. Fast kinetics-based biochemical assays demonstrate that the Δ 50S subunit is only 50% active and two times slower than the WT 50S subunit in rapid subunit association. While the Δ 70S ribosomes show no defect in peptide bond formation, peptide release, and ribosome recycling, they translocate with 20% slower rate than the WT ribosomes in each round of elongation. These defects amplify during synthesis of the full-length proteins and cause overall defect in protein synthesis. In conclusion, our data reveal the molecular roles of U2552 methylation in both ribosome biogenesis and protein translation.

PubMed: 32571953
DOI: 10.1073/pnas.1914323117

Experimental method

ELECTRON MICROSCOPY (3.14 Å)