Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes

Abstract

SummaryIn eukaryotes, accurate protein synthesis relies on a family of translational GTPases that pair with specific decoding factors to decipher the mRNA code on ribosomes. We present structures of the mammalian ribosome engaged with decoding factor⋅GTPase complexes representing intermediates of translation elongation (aminoacyl-tRNA⋅eEF1A), termination (eRF1⋅eRF3), and ribosome rescue (Pelota⋅Hbs1l). Comparative analyses reveal that each decoding factor exploits the plasticity of the ribosomal decoding center to differentially remodel ribosomal proteins and rRNA. This leads to varying degrees of large-scale ribosome movements and implies distinct mechanisms for communicating information from the decoding center to each GTPase. Additional structural snapshots of the translation termination pathway reveal the conformational changes that choreograph the accommodation of decoding factors into the peptidyl transferase center. Our results provide a structural framework for how different states of the mammalian ribosome are selectively recognized by the appropriate decoding factor⋅GTPase complex to ensure translational fidelity.

GTP Hydrolysis by eIF5B in the Last Step of Translation Initiation Is Activated by a Rotation of the Small Ribosomal Subunit

“…In this activated conformation, the histidine is seen to coordinate a water molecule that is in position for hydrolysis of the γ-phosphate of GTP [11]. This mechanism for GTPase activity seems to be conserved from Bacteria to Eukarya as several high resolution cryoEM structures of ribosome-GTPase complexes from yeast as well as mammals agree well with the initial model derived from Xray crystallography of a bacterial complex [15,16]. In the case of eIF5B, the equivalent histidine (His480, S.cerevisiae numbering) is stabilized in a similar activated conformation.…”

The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs

“…The coaxially aligned SL‐III and ASL‐like domain forms a straight unit of shape and dimensions similar to a tRNA, excluding the acceptor stem (Fig C). Alignments of structures containing tRNAs in several configurations [canonical tRNA PDBID:4V5D (Voorhees et al , ), with A/T‐tRNA PDBID:5LZS (Shao et al , ) and hybrid tRNA PDBID:3J7R (Voorhees et al , )] with the structure of the IAPV‐IRES in complex with the 40S, reveal an interesting positioning of the coaxial unit formed by SL‐III and the ASL‐like part of PKI (Fig C). Notably, the SL‐III/ASL‐like unit of IAPV‐IRES populates a space more similar to a hybrid A/P‐tRNA than a canonical, A/A‐tRNA or A/T‐tRNA [following nomenclature of hybrid states previously proposed (Ratje et al , )].…”

Long non‐coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution

“…Sequence analysis shows that the corresponding sequences in the 3 0 SLs of DENV2 and ZIKV are not conserved ( Fig 7G); therefore, the potential interaction between the sHP and SL is not a conserved feature among flavivirus genomes. Recently, the high-resolution structure of mammalian eEF1A bound to ribosome was solved by cryo-EM [64], which consists of three subdomains that folds into a compact structure with a calculated D max of 75.4 Å (Fig 7F). Several host and viral proteins, including NS5, NS3, La autoantigen, and eEF1A, have been identified to interact with sfRNAs/3 0 UTR at the 3 0 SL site [21], but the structural basis of the interactions is unknown yet.…”