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Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution

Author

Listed:
  • Zhaoming Su

    (Sichuan University
    Stanford University)

  • Kaiming Zhang

    (Stanford University
    University of Science and Technology of China)

  • Kalli Kappel

    (Stanford University)

  • Shanshan Li

    (Stanford University
    University of Science and Technology of China)

  • Michael Z. Palo

    (Stanford University)

  • Grigore D. Pintilie

    (Stanford University)

  • Ramya Rangan

    (Stanford University)

  • Bingnan Luo

    (Sichuan University)

  • Yuquan Wei

    (Sichuan University)

  • Rhiju Das

    (Stanford University
    Stanford University)

  • Wah Chiu

    (Stanford University
    SLAC National Accelerator Laboratory)

Abstract

Single-particle cryogenic electron microscopy (cryo-EM) has become a standard technique for determining protein structures at atomic resolution1–3. However, cryo-EM studies of protein-free RNA are in their early days. The Tetrahymena thermophila group I self-splicing intron was the first ribozyme to be discovered and has been a prominent model system for the study of RNA catalysis and structure–function relationships4, but its full structure remains unknown. Here we report cryo-EM structures of the full-length Tetrahymena ribozyme in substrate-free and bound states at a resolution of 3.1 Å. Newly resolved peripheral regions form two coaxially stacked helices; these are interconnected by two kissing loop pseudoknots that wrap around the catalytic core and include two previously unforeseen (to our knowledge) tertiary interactions. The global architecture is nearly identical in both states; only the internal guide sequence and guanosine binding site undergo a large conformational change and a localized shift, respectively, upon binding of RNA substrates. These results provide a long-sought structural view of a paradigmatic RNA enzyme and signal a new era for the cryo-EM-based study of structure–function relationships in ribozymes.

Suggested Citation

  • Zhaoming Su & Kaiming Zhang & Kalli Kappel & Shanshan Li & Michael Z. Palo & Grigore D. Pintilie & Ramya Rangan & Bingnan Luo & Yuquan Wei & Rhiju Das & Wah Chiu, 2021. "Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution," Nature, Nature, vol. 596(7873), pages 603-607, August.
  • Handle: RePEc:nat:nature:v:596:y:2021:i:7873:d:10.1038_s41586-021-03803-w
    DOI: 10.1038/s41586-021-03803-w
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    Cited by:

    1. Tao Li & Hong Cao & Jiahua He & Sheng-You Huang, 2024. "Automated detection and de novo structure modeling of nucleic acids from cryo-EM maps," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Lauren Gambill & August Staubus & Kim Wai Mo & Andrea Ameruoso & James Chappell, 2023. "A split ribozyme that links detection of a native RNA to orthogonal protein outputs," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    3. Shanshan Li & Michael Z. Palo & Xiaojing Zhang & Grigore Pintilie & Kaiming Zhang, 2023. "Snapshots of the second-step self-splicing of Tetrahymena ribozyme revealed by cryo-EM," Nature Communications, Nature, vol. 14(1), pages 1-10, December.

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