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Structural characterization of ribosome recruitment and translocation by type IV IRES.

<div class='caption-title'>(A) Schematic representation of the type-IV IRES, colored according to different structural motifs. (B) Overall view of the interaction of the CrPV-IRES PKI (colored as in (A) in the context of the small ribosomal subunit (40S, yellow). On the left, experimental density is shown in the same orientation as on the right, where the final refined model is depicted. (C) Schematic view of PKI with main components labelled. (D) Space-filling models for the base pairs established between the anticodon and codon mimics of PKI (BP1-3) as well as the adjacent base pair (BP4).</div>
<div class='caption-title'>EM image processing workflow for the CrPV-IRES/40S data.</div>
<div class='caption-title'>(A) Fourier shell correlation (FSC) of two independent half-maps for the complex CrPV-IRES/40S from the final refined class of particles. (B) FSC calculated for the refined model and the final map (black line). For cross-validation, the FSC calculated against a model refined with a half map (red line) is compared with the FSC calculated with the half map not included in the refinement (blue line). The overlapping of both lines provides evidence for the absence of overfitting in the refined model. (C) Unsharpened map colored according to the computed local resolution for the final map for the CrPV-IRES in the binary CrPV-IRES/40S complex. (D) Refined model of CrPV-IRES colored according to the atomic B-factor values (blue low, red high). (E) Fourier shell correlation (FSC) of two independent half-maps for the complex 80S/CrPV-IRES/eEF2 from the final refined class of particles. (F) FSC calculated for the refined model and the final map (black lane). Cross-validation by comparing the FSC calculated against a model refined with a half map (red line) and the FSC calculated with the half map not included in the refinement (blue line). (G) Unsharpened map colored according to the computed local resolution for the final map for the CrPV-IRES and eEF2. (H) Refined model of eEF2 coloured according to the atomic B-factor values (blue low, red high).</div>
Murray J, Savva CG, Shin BS, Dever TE, Ramakrishnan V, Fernández IS
OpenAccess logo Elife 5 (2016)
Cited: 55 times
EuropePMC logo PMID: 27159451

Abstract

Viral mRNA sequences with a type IV IRES are able to initiate translation without any host initiation factors. Initial recruitment of the small ribosomal subunit as well as two translocation steps before the first peptidyl transfer are essential for the initiation of translation by these mRNAs. Using electron cryomicroscopy (cryo-EM) we have structurally characterized at high resolution how the Cricket Paralysis Virus Internal Ribosomal Entry Site (CrPV-IRES) binds the small ribosomal subunit (40S) and the translocation intermediate stabilized by elongation factor 2 (eEF2). The CrPV-IRES restricts tvhe otherwise flexible 40S head to a conformation compatible with binding the large ribosomal subunit (60S). Once the 60S is recruited, the binary CrPV-IRES/80S complex oscillates between canonical and rotated states (Fernández et al., 2014; Koh et al., 2014), as seen for pre-translocation complexes with tRNAs. Elongation factor eEF2 with a GTP analog stabilizes the ribosome-IRES complex in a rotated state with an extra ~3 degrees of rotation. Key residues in domain IV of eEF2 interact with pseudoknot I (PKI) of the CrPV-IRES stabilizing it in a conformation reminiscent of a hybrid tRNA state. The structure explains how diphthamide, a eukaryotic and archaeal specific post-translational modification of a histidine residue of eEF2, is involved in translocation.

Articles - 5it7 mentioned but not cited (4)

  1. Structural characterization of ribosome recruitment and translocation by type IV IRES. Murray J, Savva CG, Shin BS, Dever TE, Ramakrishnan V, Fernández IS. Elife 5 e13567 (2016)
  2. tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis. Flis J, Holm M, Rundlet EJ, Loerke J, Hilal T, Dabrowski M, Bürger J, Mielke T, Blanchard SC, Spahn CMT, Budkevich TV. Cell Rep 25 2676-2688.e7 (2018)
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