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3fik

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3fik, resolution 6.70Å ()
Related: 2i2v, 3fih
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


Contents

Ternary complex-bound E.coli 70S ribosome. This entry consists of the 50S subunit.

Publication Abstract from PubMed

In translation, elongation factor Tu (EF-Tu) molecules deliver aminoacyl-tRNAs to the mRNA-programmed ribosome. The GTPase activity of EF-Tu is triggered by ribosome-induced conformational changes of the factor that play a pivotal role in the selection of the cognate aminoacyl-tRNAs. We present a 6.7-A cryo-electron microscopy map of the aminoacyl-tRNA x EF-Tu x GDP x kirromycin-bound Escherichia coli ribosome, together with an atomic model of the complex obtained through molecular dynamics flexible fitting. The model reveals the conformational changes in the conserved GTPase switch regions of EF-Tu that trigger hydrolysis of GTP, along with key interactions, including those between the sarcin-ricin loop and the P loop of EF-Tu, and between the effector loop of EF-Tu and a conserved region of the 16S rRNA. Our data suggest that GTP hydrolysis on EF-Tu is controlled through a hydrophobic gate mechanism.

Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis., Villa E, Sengupta J, Trabuco LG, LeBarron J, Baxter WT, Shaikh TR, Grassucci RA, Nissen P, Ehrenberg M, Schulten K, Frank J, Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):1063-8. Epub 2009 Jan 2. PMID:19122150

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

3fik is a 31 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA.

See Also

Reference

  • Villa E, Sengupta J, Trabuco LG, LeBarron J, Baxter WT, Shaikh TR, Grassucci RA, Nissen P, Ehrenberg M, Schulten K, Frank J. Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):1063-8. Epub 2009 Jan 2. PMID:19122150
  • Trabuco LG, Villa E, Mitra K, Frank J, Schulten K. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure. 2008 May;16(5):673-83. PMID:18462672 doi:10.1016/j.str.2008.03.005
  • LeBarron J, Grassucci RA, Shaikh TR, Baxter WT, Sengupta J, Frank J. Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome. J Struct Biol. 2008 Oct;164(1):24-32. Epub 2008 Jun 18. PMID:18606549 doi:10.1016/j.jsb.2008.05.007

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