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TitleVisualization of the eEF2-80S ribosome transition-state complex by cryo-electron microscopy.
Journal, issue, pagesJ Mol Biol, Vol. 382, Issue 1, Page 179-187, Year 2008
Publish dateSep 26, 2008
AuthorsJayati Sengupta / Jakob Nilsson / Richard Gursky / Morten Kjeldgaard / Poul Nissen / Joachim Frank /
PubMed AbstractIn an attempt to understand ribosome-induced GTP hydrolysis on eEF2, we determined a 12.6-A cryo-electron microscopy reconstruction of the eEF2-bound 80S ribosome in the presence of aluminum ...In an attempt to understand ribosome-induced GTP hydrolysis on eEF2, we determined a 12.6-A cryo-electron microscopy reconstruction of the eEF2-bound 80S ribosome in the presence of aluminum tetrafluoride and GDP, with aluminum tetrafluoride mimicking the gamma-phosphate during hydrolysis. This is the first visualization of a structure representing a transition-state complex on the ribosome. Tight interactions are observed between the factor's G domain and the large ribosomal subunit, as well as between domain IV and an intersubunit bridge. In contrast, some of the domains of eEF2 implicated in small subunit binding display a large degree of flexibility. Furthermore, we find support for a transition-state model conformation of the switch I region in this complex where the reoriented switch I region interacts with a conserved rRNA region of the 40S subunit formed by loops of the 18S RNA helices 8 and 14. This complex is structurally distinct from the eEF2-bound 80S ribosome complexes previously reported, and analysis of this map sheds light on the GTPase-coupled translocation mechanism.
External linksJ Mol Biol / PubMed:18644383 / PubMed Central
MethodsEM (single particle)
Resolution12.6 - 15.3 Å
Structure data

5015

3dwu

EMDB-5015: A 12.6A cryo-EM map of the 80S.eEF2.AlF4-GDP complex
PDB-3dwu: Transition-state model conformation of the switch I region fitted into the cryo-EM map of the eEF2.80S.AlF4.GDP complex
Method: EM (single particle) / Resolution: 12.6 Å

EMDB-5016:
15.3A eEF2-80S Ribosome Transition State Complex by Cryo-electron Microscopy
Method: EM (single particle) / Resolution: 15.3 Å

5017

3dny

3dwu

EMDB-5017: Segmented eEF2 density from the cryo-EM map of eEF2-bound 80S complex
PDB-3dny: Fitting of the eEF2 crystal structure into the cryo-EM density map of the eEF2.80S.AlF4-.GDP complex
PDB-3dwu: Transition-state model conformation of the switch I region fitted into the cryo-EM map of the eEF2.80S.AlF4.GDP complex
Method: EM (single particle) / Resolution: 12.6 Å

Source
  • Thermomyces lanuginosus (fungus)
  • saccharomyces cerevisiae (brewer's yeast)
  • thermus thermophilus hb8 (bacteria)
KeywordsCELL CYCLE / eEF2 transition state complex / 80S Ribosome / AlF4- / GDP / GTPase / Translocation / Elongation factor / GTP-binding / Nucleotide-binding / Phosphoprotein / Protein biosynthesis / RNA-binding / rRNA-binding / BIOSYNTHETIC PROTEIN / Transition state / conserved switch I / Antibiotic resistance / Membrane / Methylation

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