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Structure paper

TitleCryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A.
Journal, issue, pagesNucleic Acids Res, Vol. 46, Issue 11, Page 5861-5874, Year 2018
Publish dateJun 20, 2018
AuthorsMarcus Fislage / Jingji Zhang / Zuben Patrick Brown / Chandra Sekhar Mandava / Suparna Sanyal / Måns Ehrenberg / Joachim Frank /
PubMed AbstractThe GTPase EF-Tu in ternary complex with GTP and aminoacyl-tRNA (aa-tRNA) promotes rapid and accurate delivery of cognate aa-tRNAs to the ribosomal A site. Here we used cryo-EM to study the molecular ...The GTPase EF-Tu in ternary complex with GTP and aminoacyl-tRNA (aa-tRNA) promotes rapid and accurate delivery of cognate aa-tRNAs to the ribosomal A site. Here we used cryo-EM to study the molecular origins of the accuracy of ribosome-aided recognition of a cognate ternary complex and the accuracy-amplifying role of the monitoring bases A1492, A1493 and G530 of the 16S rRNA. We used the GTPase-deficient EF-Tu variant H84A with native GTP, rather than non-cleavable GTP analogues, to trap a near-cognate ternary complex in high-resolution ribosomal complexes of varying codon-recognition accuracy. We found that ribosome complexes trapped by GTPase-deficicent ternary complex due to the presence of EF-TuH84A or non-cleavable GTP analogues have very similar structures. We further discuss speed and accuracy of initial aa-tRNA selection in terms of conformational changes of aa-tRNA and stepwise activation of the monitoring bases at the decoding center of the ribosome.
External linksNucleic Acids Res / PubMed:29733411 / PubMed Central
MethodsEM (single particle)
Resolution3.0 - 3.6 Å
Structure data

8813

5wdt

EMDB-8813, PDB-5wdt:
70S ribosome-EF-Tu H84A complex with GppNHp
Method: EM (single particle) / Resolution: 3.0 Å

8814

5we4

EMDB-8814: 70S ribosome-EF-Tu H84A complex with GppNHp
PDB-5we4: 70S ribosome-EF-Tu wt complex with GppNHp
Method: EM (single particle) / Resolution: 3.1 Å

8815

5we6

EMDB-8815, PDB-5we6:
70S ribosome-EF-Tu H84A complex with GTP and cognate tRNA
Method: EM (single particle) / Resolution: 3.4 Å

8826

5wf0

EMDB-8826, PDB-5wf0:
70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C2)
Method: EM (single particle) / Resolution: 3.6 Å

8828

5wfk

EMDB-8828, PDB-5wfk:
70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C3)
Method: EM (single particle) / Resolution: 3.4 Å

8829

5wfs

EMDB-8829: 70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex III)
PDB-5wfs: 70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C4)
Method: EM (single particle) / Resolution: 3.0 Å

Chemicals

ChemComp-FME:
N-FORMYLMETHIONINE / N-Formylmethionine

ChemComp-MG:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-PHE:
PHENYLALANINE / Phenylalanine

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

ChemComp-HOH:
WATER / Water

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

Source
  • escherichia coli (E. coli)
  • escherichia coli (strain k12) (bacteria)
  • Escherichia coli
  • escherichia coli o139:h28 (strain e24377a / etec) (bacteria)
KeywordsRIBOSOME / translation / GTPase

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