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The chemical landscape of the human ribosome at 1.67 Å resolution

View ORCID ProfileAlexandre Faille, Kyle C. Dent, View ORCID ProfileSimone Pellegrino, View ORCID ProfilePekka Jaako, View ORCID ProfileAlan J Warren
doi: https://doi.org/10.1101/2023.02.28.530191
Alexandre Faille
1Cambridge Institute for Medical Research, Cambridge Biomedical Campus Keith Peters Building, Hills Rd, Cambridge CB2 0XY, United Kingdom
2Department of Haematology, University of Cambridge School of Clinical Medicine, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
3Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
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Kyle C. Dent
1Cambridge Institute for Medical Research, Cambridge Biomedical Campus Keith Peters Building, Hills Rd, Cambridge CB2 0XY, United Kingdom
2Department of Haematology, University of Cambridge School of Clinical Medicine, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
3Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
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Simone Pellegrino
1Cambridge Institute for Medical Research, Cambridge Biomedical Campus Keith Peters Building, Hills Rd, Cambridge CB2 0XY, United Kingdom
2Department of Haematology, University of Cambridge School of Clinical Medicine, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
3Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
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Pekka Jaako
1Cambridge Institute for Medical Research, Cambridge Biomedical Campus Keith Peters Building, Hills Rd, Cambridge CB2 0XY, United Kingdom
2Department of Haematology, University of Cambridge School of Clinical Medicine, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
3Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
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Alan J Warren
1Cambridge Institute for Medical Research, Cambridge Biomedical Campus Keith Peters Building, Hills Rd, Cambridge CB2 0XY, United Kingdom
2Department of Haematology, University of Cambridge School of Clinical Medicine, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
3Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
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  • For correspondence: ajw1000@cam.ac.uk
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ABSTRACT

The ability of ribosomes to translate the genetic code into protein requires a finely tuned ion and solvent ecosystem. However, the lack of high-resolution structures has precluded accurate positioning of all the functional elements of the ribosome and limited our understanding of the specific role of ribosomal RNA chemical modifications in modulating ribosome function in health and disease. Here, using a new sample preparation methodology based on functionalised pristine graphene-coated grids, we solve the cryo-EM structure of the human large ribosomal subunit to a resolution of 1.67 Å. The accurate assignment of water molecules, magnesium and potassium ions in our model highlights the fundamental biological role of ribosomal RNA methylation in harnessing unconventional carbon-oxygen hydrogen bonds to establish chemical interactions with the environment and fine-tune the functional interplay with tRNA. In addition, the structures of three translational inhibitors bound to the human large ribosomal subunit at better than 2 Å resolution provide mechanistic insights into how three key druggable pockets of the ribosome are targeted and illustrate the potential of this methodology to accelerate high-throughput structure-based design of anti-cancer therapeutics.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted February 28, 2023.
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The chemical landscape of the human ribosome at 1.67 Å resolution
Alexandre Faille, Kyle C. Dent, Simone Pellegrino, Pekka Jaako, Alan J Warren
bioRxiv 2023.02.28.530191; doi: https://doi.org/10.1101/2023.02.28.530191
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The chemical landscape of the human ribosome at 1.67 Å resolution
Alexandre Faille, Kyle C. Dent, Simone Pellegrino, Pekka Jaako, Alan J Warren
bioRxiv 2023.02.28.530191; doi: https://doi.org/10.1101/2023.02.28.530191

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