7D80

Molecular model of the cryo-EM structure of 70S ribosome in complex with peptide deformylase, trigger factor, and methionine aminopeptidase

This is a non-PDB format compatible entry.

Summary for 7D80

• Entry DOI: 10.2210/pdb7d80/pdb
• EMDB information: 30598 30611
• Descriptor: 50S ribosomal protein L34, 30S ribosomal protein S3, 30S ribosomal protein S4, ... (57 entities in total)
• Functional Keywords: escherichia coli, ribosome, nascent chain, protein biogenesis, peptide deformylase, trigger factor, methionine aminopeptidase
• Biological source: Escherichia coli (strain K12); More
• Total number of polymer chains: 57
• Total formula weight: 2286206.03

Authors

Akbar, S.,Bhakta, S.,Sengupta, J. (deposition date: 2020-10-06, release date: 2021-04-07, Last modification date: 2024-05-29)

Primary citation

Akbar, S.,Bhakta, S.,Sengupta, J.
Structural insights into the interplay of protein biogenesis factors with the 70S ribosome.
Structure, 29:755-767.e4, 2021

PubMed Abstract: Bacterial co-translational N-terminal methionine excision, an early event of nascent polypeptide chain processing, is mediated by two enzymes: peptide deformylase (PDF) and methionine aminopeptidase (MetAP). Trigger factor (TF), the only ribosome-associated bacterial chaperone, offers co-translational chaperoning assistance. Here, we present two high-resolution cryoelectron microscopy structures of tRNA-bound E. coli ribosome complexes showing simultaneous binding of PDF and TF, in the absence (3.4 Å) and presence of MetAP (4.1 Å). These structures establish molecular details of the interactions of the factors with the ribosome, and thereby reveal the structural basis of nascent chain processing. Our results suggest that simultaneous binding of all three factors is not a functionally favorable mechanism of nascent chain processing. Strikingly, an unusual structural distortion of the 70S ribosome, potentially driven by binding of multiple copies of MetAP, is observed when MetAP is incubated with a pre-formed PDF-TF-bound ribosome complex.

PubMed: 33761323
DOI: 10.1016/j.str.2021.03.005

Experimental method

ELECTRON MICROSCOPY (4.1 Å)