4V69

Ternary complex-bound E.coli 70S ribosome.

This is a non-PDB format compatible entry.

Summary for 4V69

• Entry DOI: 10.2210/pdb4v69/pdb
• Related: 1ob2 2i2u 2i2v 2j00
• EMDB information: 5036
• Descriptor: 30S ribosomal protein S10, 30S ribosomal protein S19, 30S ribosomal protein S20, ... (59 entities in total)
• Functional Keywords: ribosome, ternary complex, flexible fitting, cryo-em, 30s, 50s, trna, mrna, ef-tu, 70s, ribonucleoprotein, ribosomal protein, rna-binding, rrna-binding, antibiotic resistance, repressor, transcription, transcription regulation, transcription termination, translation regulation, trna-binding, methylation, endonuclease, hydrolase, nuclease, cell membrane, elongation factor, gtp-binding, membrane, nucleotide-binding, phosphoprotein, protein biosynthesis
• Biological source: Escherichia coli; More
• Total number of polymer chains: 58
• Total formula weight: 2257224.11

Authors

Villa, E.,Sengupta, J.,Trabuco, L.G.,LeBarron, J.,Baxter, W.T.,Shaikh, T.R.,Grassucci, R.A.,Nissen, P.,Ehrenberg, M.,Schulten, K.,Frank, J. (deposition date: 2008-12-11, release date: 2014-07-09, Last modification date: 2024-02-28)

Primary citation

Villa, E.,Sengupta, J.,Trabuco, L.G.,LeBarron, J.,Baxter, W.T.,Shaikh, T.R.,Grassucci, R.A.,Nissen, P.,Ehrenberg, M.,Schulten, K.,Frank, J.
Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis
Proc.Natl.Acad.Sci.USA, 106:1063-1068, 2009

PubMed Abstract: In translation, elongation factor Tu (EF-Tu) molecules deliver aminoacyl-tRNAs to the mRNA-programmed ribosome. The GTPase activity of EF-Tu is triggered by ribosome-induced conformational changes of the factor that play a pivotal role in the selection of the cognate aminoacyl-tRNAs. We present a 6.7-A cryo-electron microscopy map of the aminoacyl-tRNA x EF-Tu x GDP x kirromycin-bound Escherichia coli ribosome, together with an atomic model of the complex obtained through molecular dynamics flexible fitting. The model reveals the conformational changes in the conserved GTPase switch regions of EF-Tu that trigger hydrolysis of GTP, along with key interactions, including those between the sarcin-ricin loop and the P loop of EF-Tu, and between the effector loop of EF-Tu and a conserved region of the 16S rRNA. Our data suggest that GTP hydrolysis on EF-Tu is controlled through a hydrophobic gate mechanism.

PubMed: 19122150
DOI: 10.1073/pnas.0811370106

Experimental method

ELECTRON MICROSCOPY (6.7 Å)