Dynamic association of human Ebp1 with the ribosome

Abstract

Ribosomes are the macromolecular machines at the heart of protein synthesis, however, their function can be modulated by a variety of additional protein factors that directly interact with them. Here, we report the cryo-EM structure of human Ebp1 (p48 isoform) bound to the human 80S ribosome at 3.3 Å resolution. Ebp1 binds in the vicinity of the peptide exit tunnel on the 80S ribosome and this binding is enhanced upon puromycin-mediated translational inhibition. The association of Ebp1 with the 80S ribosome centers around its interaction with ribosomal proteins eL19 and uL23 and the 28S rRNA. Further analysis of the Ebp1-ribosome complex suggests that Ebp1 can rotate around its insert domain, which may enable it assume a wide range of conformations while maintaining its interaction with the ribosome. Structurally, Ebp1 shares homology with the methionine aminopeptidase 2 family of enzymes, therefore, this inherent flexibility may also be conserved.

Neuronal RNA granules are ribosome complexes stalled at the pre-translocation state

“…Likewise, the crosslink of Ttc5 to uL24 agrees with the data of Lin and coworkers showing uL24 as the unique protein binding partner of Ttc5 near the peptide exit site (Lin et al, 2020). Similarly, the cross-link between K238 of Pa2g4 and K43 of uL29 places Pa2g4 close to the peptide exit site on the 60S subunit and within an interaction distance of eL19, uL23 and uL29 as was observed by translationally inactive 80S ribosome (Bhaskar et al, 2021). In addition to those RBPs, we identified cross-links between r-proteins and proteins involved in ribosome biogenesis (Pelp1, Gtpbp4, Nop58), ubiquitin-dependent protein degradation (Zer1) as well as RNA splicing (Nop58, Hnrnpc, Snu13, Sf3bf3) and stress granule assembly (Casc3).…”

Neuronal RNA granules are ribosome complexes stalled at the pre-translocation state

“…Likewise, the crosslink of Ttc5 to uL24 agrees with the data of Lin and coworkers showing uL24 as the unique protein binding partner of Ttc5 near the peptide exit site (Lin et al, 2020). Similarly, the cross-link between K238 of Pa2g4 and K43 of uL29 places Pa2g4 close to the peptide exit site on the 60S subunit and within an interaction distance of eL19, uL23 and uL29 as was observed by translationally inactive 80S ribosome (Bhaskar et al, 2021).…”

Ribosome biogenesis factors—from names to functions

“…One notable exception is PA2G4/EBP1, which is significantly smaller than its yeast homolog Arx1. PA2G4 has been implicated both in ribosome biogenesis and translation, as it was shown to bind to pre‐60S as well as mature 80S ribosomes in vivo (Liang et al , 2020 ; Bhaskar et al , 2021 ; Kraushar et al , 2021 ). Several structural features of yeast Arx1 that might play a role in 60S biogenesis are missing in PA2G4.…”