Comprehensive Molecular Structure of the Eukaryotic Ribosome

Taylor, Derek; Devkota, Batsal; Huang, Aiping; Topf, Maya; Eswar, Narayanan; Šali, Andrej; Harvey, Stephen C.; Frank, Joachim

doi:10.1016/j.str.2009.09.015

Cited by 146 publications

(178 citation statements)

References 77 publications

(112 reference statements)

Supporting

Mentioning

173

Contrasting

Order By: Relevance

“…4A), as predicted previously by Alkemar and Nygård (25). Although this interaction was not modeled in the fungal or canine 80S ribosomes (23,24), covariation analysis suggests that the ES3 S -ES6 S base-pairing interaction is also conserved in mammalian 80S ribosomes (25).…”

Section: Comparison Of Expansion Segments Between Yeast and Wheat Germsupporting

confidence: 74%

“…Recently, a more comprehensive model of the yeast S. cerevisiae ribosome was built on the basis of an 8.9-Å cryo-EM reconstruction of a 80S ribosome from a related thermophilic fungus, Thermomyces lanuginosus (24), which, however, shares only ∼85% sequence identity with S. cerevisiae rRNA. With the exception of ES10 L , ES27 L , and the tip of ES15 L , molecular models were built for all the remaining expansion segments and variable regions (24). Yet, a number of significant differences between the yeast model presented by Taylor et al (24) and the yeast model presented here are evident (Fig.…”

Section: Comparison Of Expansion Segments Between Yeast and Wheat Germmentioning

confidence: 70%

“…Initial core models for the yeast 80S ribosome were built at 15-Å resolution (22) by docking the rRNA structures of the bacterial small 30S subunit (6) and archaeal large 50S subunit (8), as well as docking of corresponding homology models of the r proteins. Recently, reconstructions at about 9-Å resolution of fungal and dog 80S ribosomes were used to extend the molecular models to include rRNA expansion segments (23,24). However, due to the modest resolution, the completeness and accuracy of these models are also limited.…”

mentioning

confidence: 99%

See 2 more Smart Citations

Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-Å resolution

Armache

Jarasch

Anger

et al. 2010

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

204

198

View full text Add to dashboard Cite

Protein biosynthesis, the translation of the genetic code into polypeptides, occurs on ribonucleoprotein particles called ribosomes. Although X-ray structures of bacterial ribosomes are available, high-resolution structures of eukaryotic 80S ribosomes are lacking. Using cryoelectron microscopy and single-particle reconstruction, we have determined the structure of a translating plant (Triticum aestivum) 80S ribosome at 5.5-Å resolution. This map, together with a 6.1-Å map of a Saccharomyces cerevisiae 80S ribosome, has enabled us to model ∼98% of the rRNA. Accurate assignment of the rRNA expansion segments (ES) and variable regions has revealed unique ES-ES and r-protein-ES interactions, providing insight into the structure and evolution of the eukaryotic ribosome.modeling | molecular dynamics | flexible fitting I n all living cells, the translation of mRNA into polypeptide occurs on ribosomes. Ribosomes provide a platform upon which aminoacyl-tRNAs interact with the mRNA as well as position the aminoacyl-tRNAs for peptide-bond formation (1). Ribosomes are composed of two subunits, a small subunit that monitors the mRNA-tRNA codon-anticodon duplex to ensure fidelity of decoding (2, 3) and a large subunit that contains the active site where peptide-bond formation occurs (4). Both the small and large subunits are composed of RNA and protein: In eubacteria such as Escherichia coli, the small subunit contains one 16S rRNA and 21 ribosomal proteins (r proteins), whereas the large subunit contains 5S and 23S rRNAs and 33 r proteins. Crystal structures of the complete bacterial 70S ribosome were initially reported at 5.5 Å (5), with an interpretation based on atomic models of the individual subunit structures (6-8), and are now available at atomic resolution (9). These structures have provided unparalleled insight into the mechanism of different steps of translation (1) as well as inhibition by antibiotics (10).Compared to the bacterial ribosome, the eukaryotic counterpart is more complicated, containing expansion segments (ES) and variable regions in the rRNA as well as many additional r proteins and r-protein extensions. Plant and fungal 80S ribosomes contain ∼5;500 nucleotides (nts) of rRNA and ∼80 r proteins, whereas bacterial 70S ribosomes comprise ∼4;500 nts and 54 r proteins. The additional elements present in eukaryotic ribosomes may reflect the increased complexity of translation regulation in eukaryotic cells, as evident for assembly, translation initiation, and development, as well as the phenomenon of localized translation (11-15).Early models for eukaryotic ribosomes were derived from electron micrographs of negative-stain or freeze-dried ribosomal particles (16) and localization of r proteins was attempted using immuno-EM and cross-linking approaches; see, for example, refs. 17-20. The first cryo-EM reconstruction of a eukaryotic 80S ribosome was reported for wheat germ (Triticum aestivum) at 38 Å (21). Initial core models for the yeast 80S ribosome were built at 15-Å resolution (22) by docking the rRNA s...

show abstract

Section: Comparison Of Expansion Segments Between Yeast and Wheat Germsupporting

confidence: 74%

Section: Comparison Of Expansion Segments Between Yeast and Wheat Germmentioning

confidence: 70%

mentioning

confidence: 99%

See 1 more Smart Citation

Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-Å resolution

Armache

Jarasch

Anger

et al. 2010

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

204

198

View full text Add to dashboard Cite

show abstract

“…Using rigid-body fitting of domains while making use of a published cryo-EM map of the yeast ribosome (26) for reference, we observe combinations of four motions previously described in the literature and associated with the elongation cycle, as follows: (i) ratchet-like intersubunit rotation, a counterclockwise rotation of the small subunit about an axis normal to the subunit interface (Fig. 3A, solvent view) (27,28); (ii) rotation (closing movement) of the L1 stalk toward the intersubunit space (Fig.…”

Section: Resultsmentioning

confidence: 99%

Trajectories of the ribosome as a Brownian nanomachine

Dashti

Schwander

Langlois

et al. 2014

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

Self Cite

229

222

View full text Add to dashboard Cite

A Brownian machine, a tiny device buffeted by the random motions of molecules in the environment, is capable of exploiting these thermal motions for many of the conformational changes in its work cycle. Such machines are now thought to be ubiquitous, with the ribosome, a molecular machine responsible for protein synthesis, increasingly regarded as prototypical. Here we present a new analytical approach capable of determining the free-energy landscape and the continuous trajectories of molecular machines from a large number of snapshots obtained by cryogenic electron microscopy. We demonstrate this approach in the context of experimental cryogenic electron microscope images of a large ensemble of nontranslating ribosomes purified from yeast cells. The freeenergy landscape is seen to contain a closed path of low energy, along which the ribosome exhibits conformational changes known to be associated with the elongation cycle. Our approach allows model-free quantitative analysis of the degrees of freedom and the energy landscape underlying continuous conformational changes in nanomachines, including those important for biological function.cryo-electron microscopy | elongation cycle | manifold embedding | nanomachines | translation

show abstract

“…7), although the studies reported here do not provide any evidence for such dimerization. On the basis of the crystal structure of RPS19 from Pyrococcus abyssi, cryoelectron microscopy (cryo-EM) mapping, and the x-ray structure of the yeast ribosome, the location of RPS19 has been mapped to the head region of the 40 S subunit where it is accessible for interaction with other molecules (61,62). It is likely that the N-RPS19 interaction would recruit N at the head region of the 40 S subunit.…”

Section: Discussionmentioning

confidence: 99%

Characterization of the Interaction between Hantavirus Nucleocapsid Protein (N) and Ribosomal Protein S19 (RPS19)

Cheng

Haque

Rimmer

et al. 2011

Journal of Biological Chemistry

View full text Add to dashboard Cite

Hantaviruses, members of the Bunyaviridae family, are negative-stranded emerging RNA viruses and category A pathogens that cause serious illness when transmitted to humans through aerosolized excreta of infected rodent hosts. Hantaviruses have evolved a novel translation initiation mechanism, operated by nucleocapsid protein (N), which preferentially facilitates the translation of viral mRNAs. N binds to the ribosomal protein S19 (RPS19), a structural component of the 40 S ribosomal subunit. In addition, N also binds to both the viral mRNA 5 cap and a highly conserved triplet repeat sequence of the viral mRNA 5 UTR. The simultaneous binding of N at both the terminal cap and the 5 UTR favors ribosome loading on viral transcripts during translation initiation. We characterized the binding between N and RPS19 and demonstrate the role of the N-RPS19 interaction in N-mediated translation initiation mechanism. We show that N specifically binds to RPS19 with high affinity and a binding stoichiometry of 1:1. The N-RPS19 interaction is an enthalpy-driven process. RPS19 undergoes a conformational change after binding to N. Using T7 RNA polymerase, we synthesized the hantavirus S segment mRNA, which matches the transcript generated by the viral RNA-dependent RNA polymerase in cells. We show that the N-RPS19 interaction plays a critical role in the translation of this mRNA both in cells and rabbit reticulocyte lysates. Our results demonstrate that the N-mediated translation initiation mechanism, which lures the host translation machinery for the preferential translation of viral transcripts, primarily depends on the N-RPS19 interaction. We suggest that the N-RPS19 interaction is a novel target to shut down the N-mediated translation strategy and hence virus replication in cells.Hantaviruses, members of the Bunyaviridae family, are category A pathogens and causative agents of two emerging diseases: hemorrhagic fever with renal syndrome and hantavirus cardiopulmonary syndrome with mortalities of 15 and 50%, respectively (1, 2). Hantaviruses are transmitted to humans through aerosolized excreta of infected rodent hosts. The spherical hantavirus particles harbor three negative sense genomic RNA segments (S, L, and M) within a lipid bilayer (3). The mRNAs derived from S, L, and M segments encode viral nucleocapsid protein (N), 2 viral RNA-dependent RNA polymerase (RdRp), and glycoprotein precursor, respectively. The glycoprotein precursor is cleaved at a conserved WAASA site, and two glycoproteins, Gn and Gc, are generated (4). The characteristic feature of the hantaviral genome is the partially complementary sequence at the 5Ј and 3Ј termini of each of the three genome segments that undergo base pairing and form panhandle structures (5-7). N is a multifunctional protein playing vital roles in multiple processes of the virus replication cycle and enters the host cell along with viral capsid during infection. N has been found to undergo trimerization both in vivo and in vitro (8 -20). During encapsidation, N specifically recogniz...

show abstract

Comprehensive Molecular Structure of the Eukaryotic Ribosome

Cited by 146 publications

References 77 publications

Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-Å resolution

Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-Å resolution

Trajectories of the ribosome as a Brownian nanomachine

Characterization of the Interaction between Hantavirus Nucleocapsid Protein (N) and Ribosomal Protein S19 (RPS19)

Contact Info

Product

Resources

About