EMD-8123

Single-particle
3.6 Å
EMD-8123 Deposition: 13/04/2016
Map released: 18/05/2016
Last modified: 21/11/2018
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-8123

Structure of the Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis virus IRES and eEF2

EMD-8123

Single-particle
3.6 Å
EMD-8123 Deposition: 13/04/2016
Map released: 18/05/2016
Last modified: 21/11/2018
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Yeast, Cricket paralysis virus, Saccharomyces cerevisiae P283, Baker's yeast
Sample: eEF2
Fitted models: 5it7 (Avg. Q-score: 0.358)

Deposition Authors: Murray J, Savva CG, Shin BS, Dever TE, Ramakrishnan V, Fernandez IS
Structural characterization of ribosome recruitment and translocation by type IV IRES.
PUBMED: 27159451
DOI: doi:10.7554/eLife.13567
ISSN: 2050-084X
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.