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Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome

Archaeal ribosomes have many domain-specific features; however, our understanding of these structures is limited. We present 10 cryo-electron microscopy (cryo-EM) structures of the archaeal ribosome from crenarchaeota Sulfolobus acidocaldarius (Sac) at 2.7–5.7 Å resolution. We observed unstable conf...

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Autores principales: Wang, Ying-Hui, Dai, Hong, Zhang, Ling, Wu, Yun, Wang, Jingfen, Wang, Chen, Xu, Cai-Huang, Hou, Hai, Yang, Bing, Zhu, Yongqun, Zhang, Xing, Zhou, Jie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10516650/
https://www.ncbi.nlm.nih.gov/pubmed/37604686
http://dx.doi.org/10.1093/nar/gkad661
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author Wang, Ying-Hui
Dai, Hong
Zhang, Ling
Wu, Yun
Wang, Jingfen
Wang, Chen
Xu, Cai-Huang
Hou, Hai
Yang, Bing
Zhu, Yongqun
Zhang, Xing
Zhou, Jie
author_facet Wang, Ying-Hui
Dai, Hong
Zhang, Ling
Wu, Yun
Wang, Jingfen
Wang, Chen
Xu, Cai-Huang
Hou, Hai
Yang, Bing
Zhu, Yongqun
Zhang, Xing
Zhou, Jie
author_sort Wang, Ying-Hui
collection PubMed
description Archaeal ribosomes have many domain-specific features; however, our understanding of these structures is limited. We present 10 cryo-electron microscopy (cryo-EM) structures of the archaeal ribosome from crenarchaeota Sulfolobus acidocaldarius (Sac) at 2.7–5.7 Å resolution. We observed unstable conformations of H68 and h44 of ribosomal RNA (rRNA) in the subunit structures, which may interfere with subunit association. These subunit structures provided models for 12 rRNA expansion segments and 3 novel r-proteins. Furthermore, the 50S–aRF1 complex structure showed the unique domain orientation of aRF1, possibly explaining P-site transfer RNA (tRNA) release after translation termination. Sac 70S complexes were captured in seven distinct steps of the tRNA translocation reaction, confirming conserved structural features during archaeal ribosome translocation. In aEF2-engaged 70S ribosome complexes, 3D classification of cryo-EM data based on 30S head domain identified two new translocation intermediates with 30S head domain tilted 5–6° enabling its disengagement from the translocated tRNA and its release post-translocation. Additionally, we observed conformational changes to aEF2 during ribosome binding and switching from three different states. Our structural and biochemical data provide new insights into archaeal translation and ribosome translocation.
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spelling pubmed-105166502023-09-23 Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome Wang, Ying-Hui Dai, Hong Zhang, Ling Wu, Yun Wang, Jingfen Wang, Chen Xu, Cai-Huang Hou, Hai Yang, Bing Zhu, Yongqun Zhang, Xing Zhou, Jie Nucleic Acids Res NAR Breakthrough Article Archaeal ribosomes have many domain-specific features; however, our understanding of these structures is limited. We present 10 cryo-electron microscopy (cryo-EM) structures of the archaeal ribosome from crenarchaeota Sulfolobus acidocaldarius (Sac) at 2.7–5.7 Å resolution. We observed unstable conformations of H68 and h44 of ribosomal RNA (rRNA) in the subunit structures, which may interfere with subunit association. These subunit structures provided models for 12 rRNA expansion segments and 3 novel r-proteins. Furthermore, the 50S–aRF1 complex structure showed the unique domain orientation of aRF1, possibly explaining P-site transfer RNA (tRNA) release after translation termination. Sac 70S complexes were captured in seven distinct steps of the tRNA translocation reaction, confirming conserved structural features during archaeal ribosome translocation. In aEF2-engaged 70S ribosome complexes, 3D classification of cryo-EM data based on 30S head domain identified two new translocation intermediates with 30S head domain tilted 5–6° enabling its disengagement from the translocated tRNA and its release post-translocation. Additionally, we observed conformational changes to aEF2 during ribosome binding and switching from three different states. Our structural and biochemical data provide new insights into archaeal translation and ribosome translocation. Oxford University Press 2023-08-22 /pmc/articles/PMC10516650/ /pubmed/37604686 http://dx.doi.org/10.1093/nar/gkad661 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle NAR Breakthrough Article
Wang, Ying-Hui
Dai, Hong
Zhang, Ling
Wu, Yun
Wang, Jingfen
Wang, Chen
Xu, Cai-Huang
Hou, Hai
Yang, Bing
Zhu, Yongqun
Zhang, Xing
Zhou, Jie
Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome
title Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome
title_full Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome
title_fullStr Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome
title_full_unstemmed Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome
title_short Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome
title_sort cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome
topic NAR Breakthrough Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10516650/
https://www.ncbi.nlm.nih.gov/pubmed/37604686
http://dx.doi.org/10.1093/nar/gkad661
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