8T8C

Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y, A-site aminoacyl-tRNA analog ACC-PMN, and P-site formyl-MFI-tripeptidyl-tRNA analog ACCA-IFMf at 2.60A resolution

This is a non-PDB format compatible entry.

Summary for 8T8C

• Entry DOI: 10.2210/pdb8t8c/pdb
• Descriptor: 23S Ribosomal RNA, 50S ribosomal protein L14, 50S ribosomal protein L15, ... (62 entities in total)
• Functional Keywords: 70s ribosome, peptidyl-trna, rna-peptide conjugate, rna modification, ft-icr mass spectrometry, formylation, ribosome
• Biological source: Escherichia coli K-12; More
• Total number of polymer chains: 112
• Total formula weight: 4431928.26

Authors

Thaler, J.,Syroegin, E.A.,Breuker, K.,Polikanov, Y.S.,Micura, R. (deposition date: 2023-06-22, release date: 2023-07-19, Last modification date: 2025-03-19)

Primary citation

Thaler, J.,Syroegin, E.A.,Breuker, K.,Polikanov, Y.S.,Micura, R.
Practical Synthesis of N -Formylmethionylated Peptidyl-tRNA Mimics.
Acs Chem.Biol., 18:2233-2239, 2023

PubMed Abstract: Hydrolysis-resistant RNA-peptide conjugates that mimic peptidyl-tRNAs are frequently needed for structural and functional studies of protein synthesis in the ribosome. Such conjugates are accessible by chemical solid-phase synthesis, allowing for the utmost flexibility of both the peptide and the RNA sequence. Commonly used protection group strategies, however, have severe limitations with respect to generating the characteristic -formylmethionyl terminus because the formyl group of the conjugate synthesized at the solid support is easily cleaved during the final basic deprotection/release step. In this study, we demonstrate a simple solution to the problem by coupling appropriately activated -formyl methionine to the fully deprotected conjugate. The structural integrity of the obtained -formylmethionyl conjugate─and hence the chemoselectivity of the reaction─were verified by Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry sequence analysis. Additionally, we confirmed the applicability of our procedure for structural studies by obtaining two structures of the ribosome in complex with either fMAI-nh-ACCA or fMFI-nh-ACCA in the P site and ACC-PMN in the A site of the bacterial ribosome at 2.65 and 2.60 Å resolution, respectively. In summary, our approach for hydrolysis-resistant -formylated RNA-peptide conjugates is synthetically straightforward and opens up new avenues to explore ribosomal translation with high-precision substrate mimics.

PubMed: 37433044
DOI: 10.1021/acschembio.3c00237

Experimental method

X-RAY DIFFRACTION (2.6 Å)