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Structure paper

TitleThe pathway to GTPase activation of elongation factor SelB on the ribosome.
Journal, issue, pagesNature, Vol. 540, Issue 7631, Page 80-85, Year 2016
Publish dateDec 1, 2016
AuthorsNiels Fischer / Piotr Neumann / Lars V Bock / Cristina Maracci / Zhe Wang / Alena Paleskava / Andrey L Konevega / Gunnar F Schröder / Helmut Grubmüller / Ralf Ficner / Marina V Rodnina / Holger Stark /
PubMed AbstractIn 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 ...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.
External linksNature / PubMed:27842381
MethodsEM (single particle)
Resolution3.4 - 5.3 Å
Structure data

4121

5lza

EMDB-4121, PDB-5lza:
Structure of the 70S ribosome with SECIS-mRNA and P-site tRNA (Initial complex, IC)
Method: EM (single particle) / Resolution: 3.6 Å

4122

5lzb

EMDB-4122, PDB-5lzb:
Structure of SelB-Sec-tRNASec bound to the 70S ribosome in the initial binding state (IB)
Method: EM (single particle) / Resolution: 5.3 Å

4123

5lzc

EMDB-4123, PDB-5lzc:
Structure of SelB-Sec-tRNASec bound to the 70S ribosome in the codon reading state (CR)
Method: EM (single particle) / Resolution: 4.8 Å

4124

5lzd

EMDB-4124, PDB-5lzd:
Structure of SelB-Sec-tRNASec bound to the 70S ribosome in the GTPase activated state (GA)
Method: EM (single particle) / Resolution: 3.4 Å

4125

5lze

EMDB-4125, PDB-5lze:
Structure of the 70S ribosome with Sec-tRNASec in the classical pre-translocation state (C)
Method: EM (single particle) / Resolution: 3.5 Å

4126

5lzf

EMDB-4126, PDB-5lzf:
Structure of the 70S ribosome with fMetSec-tRNASec in the hybrid pre-translocation state (H)
Method: EM (single particle) / Resolution: 4.6 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-FME:
N-FORMYLMETHIONINE / N-Formylmethionine

ChemComp-SEC:
SELENOCYSTEINE / Selenocysteine

ChemComp-GNP:
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*YM / 5'-Guanylyl imidodiphosphate

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER / Water

ChemComp-CL:
Unknown entry / Chloride

Source
  • escherichia coli (E. coli)
KeywordsRIBOSOME / translation / decoding / recoding / selenocysteine

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