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Cryo-EM structure of the RfxCas13d-crRNA-off-target-RNA complex.

Qianxi Yang1, Yifang Sun1, Lei Sun1

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Structure (London, England : 1993)
|October 24, 2025
PubMed
Summary
This summary is machine-generated.

Researchers determined cryo-EM structures of Ruminococcus flavefaciens Cas13d (RfxCas13d) in complex with RNA. This reveals how RfxCas13d binds target RNA, aiding transcriptome engineering advancements.

Keywords:
CRISPRCRISPR-CasCas13dRNA editingcryo-EM

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • CRISPR-Cas systems provide adaptive immunity in prokaryotes.
  • Cas13d is an RNA-guided ribonuclease engineered for RNA editing.
  • RfxCas13d is a well-characterized type VI editor.

Purpose of the Study:

  • To determine the cryo-EM structures of Ruminococcus flavefaciens Cas13d (RfxCas13d).
  • To elucidate the structural basis of RfxCas13d-RNA interactions.
  • To provide a framework for advancing transcriptome engineering.

Main Methods:

  • Cryo-electron microscopy (cryo-EM) was used.
  • Structures of RfxCas13d-crRNA-off-target-RNA ternary and RfxCas13d-crRNA binary complexes were determined.
  • Resolution achieved was 3.10 and 3.13 Å.

Main Results:

  • The ternary complex captured short off-target ssRNA with proximal mismatched RNA.
  • RfxCas13d exhibited conformational changes with or without off-target RNA.
  • Catalytic sites remained unchanged, and Mg2+ stabilized the crRNA repeat region.

Conclusions:

  • The structures provide insights into RfxCas13d RNA binding mechanisms.
  • This work lays the foundation for RfxCas13d as a mature transcriptome engineering tool.
  • The findings offer a framework for future advancements in RNA editing technologies.