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. 2016 Sep 11;428(18):3570-3576.
doi: 10.1016/j.jmb.2016.05.011. Epub 2016 May 16.

Crystal Structure of Hypusine-Containing Translation Factor eIF5A Bound to a Rotated Eukaryotic Ribosome

Sergey Melnikov #  1   2 , Justine Mailliot #  1   2 , Byung-Sik Shin  3 , Lukas Rigger  4 , Gulnara Yusupova  1   2 , Ronald Micura  4 , Thomas E Dever  3 , Marat Yusupov  1   2
Affiliations

Crystal Structure of Hypusine-Containing Translation Factor eIF5A Bound to a Rotated Eukaryotic Ribosome

Sergey Melnikov et al. J Mol Biol. .

Abstract

Eukaryotic translation initiation factor eIF5A promotes protein synthesis by resolving polyproline-induced ribosomal stalling. Here, we report a 3.25-Å resolution crystal structure of eIF5A bound to the yeast 80S ribosome. The structure reveals a previously unseen conformation of an eIF5A-ribosome complex and highlights a possible functional link between conformational changes of the ribosome during protein synthesis and the eIF5A-ribosome association.

Keywords: crystallography; eIF5A; hypusine; ribosome; structure.

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Figures

Fig. 1
Fig. 1. Electron density map reveals ribosome-bound eIF5A. Views of the 80S ribosome/eIF5A structure.
(a) Unbiased Fo-Fc electron density map, contoured at 3σ, reveals the hypusine conformation and allows nearly complete modeling of ribosome-bound eIF5A. Yellow cartoon traces the Cα atoms, red sticks show hypusine. (b) View of the 60S ribosomal subunit shows the eIF5A-binding site and eIF5A interactions with two dynamic ribosome features—the L1-stalk and helix H69 of the 25S rRNA. The inset shows the view orientation. (c), The hypusine-binding site. The hypusine conformation is stabilized by extensive contacts with the 25S rRNA.
Fig. 2
Fig. 2. Binding of eIF5A to the ribosome is mediated by magnesium ions.
(a) View of the eIF5A/25S rRNA interface shows two magnesium ions that stabilize the eIF5A N-terminal domain at the ribosomal interface. Arrows point to the magnesium ions. (b) The eIF5A electrostatic surface highlights positions of the magnesium ions in negatively charged cavities of the eIF5A molecule.
Fig. 3
Fig. 3. Structure of the eIF5A-binding site depends on the ribosome rotation state. Panels (a and b) illustrate that ribosome transitions between the rotated states cause marked changes in the eIF5A-binding site.
(a) The 25S rRNA from the S. cerevisiae 80S ribosome is colored by displacement of the corresponding nucleotides between the 9°/10.5° (40S rotation/40S head swivel; eIF5A-bound) and 4°/15.5° (no eIF5A) rotated states of the two ribosomes in the asymmetric unit. The most prominent difference in the eIF5A-binding site is observed in helix H69. (b) Zoom on helix H69 shows that in the eIF5A-bound ribosome, helix H69 directly contacts eIF5A, whereas in the vacant ribosome, helix H69 moves ~6 Å away when eIF5A is docked in the equivalent position. Panels (c and d) illustrate structural changes in the 25S rRNA upon eIF5A binding to the ribosome. Two crystal structures of the yeast 80S ribosome are compared: the vacant 4°/15.5°-rotated ribosome (pdb 4v7r) and the eIF5A-bound 4°/15.5°-rotated ribosome (this study). (c), The 25S rRNA from the S. cerevisiae 80S ribosome is colored as in (a). (d) Zoom on helix H69 illustrates that eIF5A binding induces relatively subtle changes in the helix H69 structure.
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References

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