3DNY

Fitting of the eEF2 crystal structure into the cryo-EM density map of the eEF2.80S.AlF4-.GDP complex

Summary for 3DNY

• Entry DOI: 10.2210/pdb3dny/pdb
• Related: 1N0U
• EMDB information: 5015 5017
• Descriptor: Elongation factor 2 (1 entity in total)
• Functional Keywords: eef2 transition state complex, 80s ribosome, alf4-, gdp, gtpase, translocation, elongation factor, gtp-binding, nucleotide-binding, phosphoprotein, protein biosynthesis, rna-binding, rrna-binding, cell cycle
• Biological source: Saccharomyces cerevisiae
• Total number of polymer chains: 1
• Total formula weight: 93407.13

Authors

Sengupta, J.,Frank, J. (deposition date: 2008-07-03, release date: 2008-08-05, Last modification date: 2024-02-21)

Primary citation

Sengupta, J.,Nilsson, J.,Gursky, R.,Kjeldgaard, M.,Nissen, P.,Frank, J.
Visualization of the eEF2-80S ribosome transition-state complex by cryo-electron microscopy.
J.Mol.Biol., 382:179-187, 2008

PubMed Abstract: 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.

PubMed: 18644383
DOI: 10.1016/j.jmb.2008.07.004

Experimental method

ELECTRON MICROSCOPY (12.6 Å)