Structure of the no-go mRNA decay complex Dom34–Hbs1 bound to a stalled 80S ribosome

Becker, Thomas; Armache, Jean-Paul; Jarasch, Alexander; Anger, A.M.; Villa, Elizabeth; Sieber, H.; Motaal, Basma Abdel; Mielke, Thorsten; Berninghausen, Otto; Beckmann, Roland

doi:10.1038/nsmb.2057

Cited by 158 publications

(198 citation statements)

References 47 publications

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“…In this orientation, the GGQ motif is situated more than 80 Å away from the PTC of the 60S subunit, which is consistent with the biochemical data, indicating that its accommodation into the PTC occurs only after GTP hydrolysis (23). A similar position has been described for the central domain of Dom34 in the yeast Hbs1-Dom34-bound No-go decay complex, also stalled in a pre-GTP hydrolysis state (29). In the docked structure of eRF1-eRF3, rpS23 (rpS12p) is nestled between the base of eRF1's domain M and domain 2 of eRF3.…”

Section: Resultssupporting

confidence: 74%

“…Although the ribosomal interactions of the eRF1-eRF3 complex described thus far are similar to those that were previously reported for the Hbs1-Dom34 and EF-Tu-tRNA complexes (28,29), there is an additional specific point of contact that involves the 40S subunit and eRF1's minidomain ( Fig. 1 C and F).…”

Section: Resultssupporting

confidence: 55%

“…Domain N is rotated by ∼100°as it reaches into the decoding center. As a result of these changes, the ribosome-bound eRF1-eRF3-GMPPNP complex adopts a conformation that is similar to those observed for bacterial 70S-bound tRNA-EF-Tu and yeast 80S-bound Dom34-Hbs1 complexes (28,29) (Fig. S3).…”

Section: Resultsmentioning

confidence: 71%

“…Our cryo-EM density maps, combined with flexible fitting of individual components determined by X-ray crystallography, revealed that eRF1-eRF3-GMPPNP bound to the pre-TC adopts a conformation that is similar to the predicted model for the eRF1-eRF3-GTP complex in solution (17), and resembles those of ribosome-bound Dom34-Hbs1-GMPPNP and tRNA-EF-Tu (28,29). In this conformation, domains M and N of eRF1 shift and rotate compared with the structure of individual eRF1 (8).…”

Section: Discussionmentioning

confidence: 99%

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Cryo-EM structure of the mammalian eukaryotic release factor eRF1–eRF3-associated termination complex

Taylor

Unbehaun

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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Eukaryotic translation termination results from the complex functional interplay between two eukaryotic release factors, eRF1 and eRF3, and the ribosome, in which GTP hydrolysis by eRF3 couples codon recognition with peptidyl-tRNA hydrolysis by eRF1. Here, using cryo-electron microscopy (cryo-EM) and flexible fitting, we determined the structure of eRF1-eRF3-guanosine 5′- [β,γ-imido] triphosphate (GMPPNP)-bound ribosomal pretermination complex (pre-TC), which corresponds to the initial, pre-GTP hydrolysis stage of factor attachment. Our results show that eukaryotic translation termination involves a network of interactions between the two release factors and the ribosome. Our structure provides mechanistic insight into the coordination between GTP hydrolysis by eRF3 and subsequent peptide release by eRF1.T ermination of translation occurs when a ribosome reaches the end of the coding region and a stop codon (UAA, UAG, or UGA) enters the aminoacyl tRNA binding site (A site), leaving peptidyl-tRNA in the peptidyl tRNA binding site (P site). It entails stop codon recognition by specialized release factors followed by hydrolysis of peptidyl-tRNA. In eukaryotes, termination is mediated by the concerted action of two directly interacting release factors, eRF1 and eRF3. eRF1 is responsible for stop codon recognition and inducing hydrolysis of peptidyl-tRNA, whereas eRF3, a ribosome-dependent GTPase, strongly stimulates peptide release by eRF1 in a GTP-dependent manner (for review, see ref. 1).eRF1 also participates in ribosome recycling: after peptide release it remains associated with the ribosome and together with ATP-binding cassette sub-family E member 1 (ABCE1) promotes splitting the ribosome into free 60S and tRNA/mRNA-associated 40S subunits (2). eRF1 and eRF3 have paralogs, Dom34 (yeast)/ Pelota (mammals) and Hbs1, respectively, which do not participate in termination but instead play a key role in No-go and nonstop decay surveillance mechanisms (e.g., see refs. 3, 4). Dom34/Pelota and Hbs1 do not induce peptide release in a mechanism similar to eRFs. Instead, they cooperate with ABCE1 to promote dissociation of stalled elongation complexes, which is accompanied by peptidyltRNA drop off (5-7). eRF1 comprises N-terminal (N), middle (M), and C-terminal (C) domains (8). The N domain is responsible for stop codon recognition, which is achieved through a 3D network of conserved residues that include apical TASNIKS (amino acid sequence: threonine-alanine-serine-asparagine-isoleucine-lysine-serine) and YxCxxxF motifs (e.g., refs. 9-12). Domain M contains the universally conserved GGQ motif, which is critical for triggering peptide release: as shown for prokaryotes, its placement into the peptidyl transferase center (PTC) causes rRNA rearrangement, allowing a water molecule to enter (for review, see ref. 13). The rigid core of domain C forms an α-β sandwich (8) that deviates from the standard form by the presence of a small insertion, which forms a minidomain (14). eRF3 consists of an N-terminal sequence (residues 1-...

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Section: Resultssupporting

confidence: 74%

Section: Resultssupporting

confidence: 55%

Section: Resultsmentioning

confidence: 71%

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Cryo-EM structure of the mammalian eukaryotic release factor eRF1–eRF3-associated termination complex

Taylor

Unbehaun

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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“…The Ski7 protein belongs to the eRF3/GSPT family based on its conserved GTPase domain. In this family, the function of two well-studied members, EF1A and eRF3, is to interact with the A site of the ribosome; thus, the GTPase domain of Ski7 is likely to be responsible for recognizing the ribosome's empty A-site during nonstop translation events, so that Ski7 can present the aberrant mRNA to Exo10 for degradation [28]. The observation that Ski7 sits on top of the exosome core indicates its role in guiding mRNA substrates to the Rrp44 RNase site via the through-core route.…”

Section: Discussionmentioning

confidence: 99%

CryoEM structure of yeast cytoplasmic exosome complex

Liu

Niu

et al. 2016

Cell Res

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The eukaryotic multi-subunit RNA exosome complex plays crucial roles in 3′-to-5′ RNA processing and decay. Rrp6 and Ski7 are the major cofactors for the nuclear and cytoplasmic exosomes, respectively. In the cytoplasm, Ski7 helps the exosome to target mRNAs for degradation and turnover via a through-core pathway. However, the interaction between Ski7 and the exosome complex has remained unclear. The transaction of RNA substrates within the exosome is also elusive. In this work, we used single-particle cryo-electron microscopy to solve the structures of the Ski7-exosome complex in RNA-free and RNA-bound forms at resolutions of 4.2 Å and 5.8 Å, respectively. These structures reveal that the N-terminal domain of Ski7 adopts a structural arrangement and interacts with the exosome in a similar fashion to the C-terminal domain of nuclear Rrp6. Further structural analysis of exosomes with RNA substrates harboring 3′ overhangs of different length suggests a switch mechanism of RNA-induced exosome activation in the through-core pathway of RNA processing.

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Ribosomal protein uS3 in cell biology and human disease: Latest insights and prospects

Graifer

Карпова

2020

BioEssays

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The conserved ribosomal protein uS3 in eukaryotes has long been known as one of the essential components of the small (40S) ribosomal subunit, which is involved in the structure of the 40S mRNA entry pore, ensuring the functioning of the 40S subunit during translation initiation. Besides, uS3, being outside the ribosome, is engaged in various cellular processes related to DNA repair, NF-kB signaling pathway and regulation of apoptosis. This review is devoted to recent data opening new horizons in understanding the roles of uS3 in such processes as the assembly and maturation of 40S subunits, ensuring proper structure of 48S pre-initiation complexes, regulation of initiation and ribosome-based RNA quality control pathways. Besides, we summarize novel results on the participation of the protein in processes beyond translation and consider biomedical implications of previously known and recently found extra-ribosomal functions of uS3, primarily, in oncogenesis.

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Structure of the no-go mRNA decay complex Dom34–Hbs1 bound to a stalled 80S ribosome

Cited by 158 publications

References 47 publications

Cryo-EM structure of the mammalian eukaryotic release factor eRF1–eRF3-associated termination complex

Cryo-EM structure of the mammalian eukaryotic release factor eRF1–eRF3-associated termination complex

CryoEM structure of yeast cytoplasmic exosome complex

Ribosomal protein uS3 in cell biology and human disease: Latest insights and prospects

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