6ENF

Cryo-EM structure of a polyproline-stalled ribosome in the absence of EF-P

This is a non-PDB format compatible entry.

Summary for 6ENF

• Entry DOI: 10.2210/pdb6enf/pdb
• EMDB information: 3898
• Descriptor: 16S ribosomal RNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... (53 entities in total)
• Functional Keywords: proline, ef-p, ribosome, nascent chain
• Biological source: Escherichia coli; More
• Total number of polymer chains: 53
• Total formula weight: 2122173.75

Authors

Huter, P.,Arenz, S.,Wilson, D.N. (deposition date: 2017-10-04, release date: 2017-11-22, Last modification date: 2024-10-23)

Primary citation

Huter, P.,Arenz, S.,Bock, L.V.,Graf, M.,Frister, J.O.,Heuer, A.,Peil, L.,Starosta, A.L.,Wohlgemuth, I.,Peske, F.,Novacek, J.,Berninghausen, O.,Grubmuller, H.,Tenson, T.,Beckmann, R.,Rodnina, M.V.,Vaiana, A.C.,Wilson, D.N.
Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P.
Mol. Cell, 68:515-527.e6, 2017

PubMed Abstract: Ribosomes synthesizing proteins containing consecutive proline residues become stalled and require rescue via the action of uniquely modified translation elongation factors, EF-P in bacteria, or archaeal/eukaryotic a/eIF5A. To date, no structures exist of EF-P or eIF5A in complex with translating ribosomes stalled at polyproline stretches, and thus structural insight into how EF-P/eIF5A rescue these arrested ribosomes has been lacking. Here we present cryo-EM structures of ribosomes stalled on proline stretches, without and with modified EF-P. The structures suggest that the favored conformation of the polyproline-containing nascent chain is incompatible with the peptide exit tunnel of the ribosome and leads to destabilization of the peptidyl-tRNA. Binding of EF-P stabilizes the P-site tRNA, particularly via interactions between its modification and the CCA end, thereby enforcing an alternative conformation of the polyproline-containing nascent chain, which allows a favorable substrate geometry for peptide bond formation.

PubMed: 29100052
DOI: 10.1016/j.molcel.2017.10.014

Experimental method

ELECTRON MICROSCOPY (3.2 Å)