Veerendra Kumar1,2, Rya Ero2, Tofayel Ahmed2, Kwok Jian Goh2, Yin Zhan2, Shashi Bhushan2,3 & Yong-Gui Gao1,2,3.
1 Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, 138673, Singapore
2 School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
3 NTU Institute of Structural Biology, Nanyang Technological University, Singapore
Published in The Journal of Biological Chemistry on 2 May 2016.
Elongation factor 4 (EF4) is a member of the family of ribosome-dependent translational GTPase (trGTPase) factors, along with elongation factor G (EF-G) and BPI-inducible protein A (BipA). Although EF4 is highly conserved in bacterial, mitochondrial, and chloroplast genomes, its exact biological function remains controversial. Here, we present the cryo-EM reconstitution of the GTP form of EF4 bound to the ribosome with P- and E-site tRNAs at 3.8 Å resolution. Interestingly, our structure reveals an unrotated ribosome rather than a clockwise-rotated ribosome, as observed in the presence of EF4-GDP and P-site tRNA. In addition, we also observed an counterclockwise rotated form of the above complex at 5.7 Å resolution. Taken together, our results shed light on the interactions formed between EF4, the ribosome, and the P-site tRNA and illuminate the GTPase activation mechanism at previously unresolved detail.
Figure Legend : Structure of the ribosome-EF4 complex. (A) Overall view of the GTP form of the EF4-ribosome complex. The EF4 protein, 50S, and 30S subunits are shown as cryo-EM densities in red, orange, and cyan, respectively. The P- and E-site tRNAs are shown as cryo-EM densities in lemon and lilac, respectively. The tRNAs are barely visible from this angle. Structural landmarks of the 50S subunit are indicated for clarity. (B and C) Ribosome ratcheting shown as rotation of the 16S rRNA in the 30S subunit relative to the 50S subunit (viewed from the solvent side of the 30S subunit). The 16S rRNAs of the present complexes of major (B) and minor (C) ribosome populations are shown in cyan and green, respectively. For comparison, the 16S rRNA (gray) in the classical unrotated ribosome with an mRNA and tRNA (26) is shown. The structures are aligned to the 23S rRNA. (D) Comparison of the 23S rRNAs in the current GTP form of the EF4-ribosome structure (orange) and in the crystal structure of GDP form of the EF4-ribosome complex (14) (gray). The ribosomal L1 and L11 stalks are labeled, and the arrows indicate the direction of the conformational change.