5LZA

Structure of the 70S ribosome with SECIS-mRNA and P-site tRNA (Initial complex, IC)

This is a non-PDB format compatible entry.

Summary for 5LZA

• Entry DOI: 10.2210/pdb5lza/pdb
• EMDB information: 4121
• Descriptor: 16S ribosomal RNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... (56 entities in total)
• Functional Keywords: translation, decoding, recoding, selenocysteine, ribosome
• Biological source: Escherichia coli; More
• Total number of polymer chains: 55
• Total formula weight: 2167401.69

Authors

Fischer, N.,Neumann, P.,Bock, L.V.,Maracci, C.,Wang, Z.,Paleskava, A.,Konevega, A.L.,Schroeder, G.F.,Grubmueller, H.,Ficner, R.,Rodnina, M.V.,Stark, H. (deposition date: 2016-09-29, release date: 2016-11-23, Last modification date: 2024-04-24)

Primary citation

Fischer, N.,Neumann, P.,Bock, L.V.,Maracci, C.,Wang, Z.,Paleskava, A.,Konevega, A.L.,Schroder, G.F.,Grubmuller, H.,Ficner, R.,Rodnina, M.V.,Stark, H.
The pathway to GTPase activation of elongation factor SelB on the ribosome.
Nature, 540:80-85, 2016

PubMed Abstract: In all domains of life, selenocysteine (Sec) is delivered to the ribosome by selenocysteine-specific tRNA (tRNA) with the help of a specialized translation factor, SelB in bacteria. Sec-tRNA recodes a UGA stop codon next to a downstream mRNA stem-loop. Here we present the structures of six intermediates on the pathway of UGA recoding in Escherichia coli by single-particle cryo-electron microscopy. The structures explain the specificity of Sec-tRNA binding by SelB and show large-scale rearrangements of Sec-tRNA. Upon initial binding of SelB-Sec-tRNA to the ribosome and codon reading, the 30S subunit adopts an open conformation with Sec-tRNA covering the sarcin-ricin loop (SRL) on the 50S subunit. Subsequent codon recognition results in a local closure of the decoding site, which moves Sec-tRNA away from the SRL and triggers a global closure of the 30S subunit shoulder domain. As a consequence, SelB docks on the SRL, activating the GTPase of SelB. These results reveal how codon recognition triggers GTPase activation in translational GTPases.

PubMed: 27842381
DOI: 10.1038/nature20560

Experimental method

ELECTRON MICROSCOPY (3.6 Å)