Summary information and primary citation

PDB-id
6iv8; DSSR-derived features in text and JSON formats
Class
RNA binding protein-RNA
Method
X-ray (2.15 Å)
Summary
The selenomethionine(semet)-derived cas13d binary complex
Reference
Zhang B, Ye Y, Ye W, Perculija V, Jiang H, Chen Y, Li Y, Chen J, Lin J, Wang S, Chen Q, Han YS, Ouyang S (2019): "Two HEPN domains dictate CRISPR RNA maturation and target cleavage in Cas13d." Nat Commun, 10, 2544. doi: 10.1038/s41467-019-10507-3.
Abstract
Cas13d, the type VI-D CRISPR-Cas effector, is an RNA-guided ribonuclease that has been repurposed to edit RNA in a programmable manner. Here we report the detailed structural and functional analysis of the uncultured Ruminococcus sp. Cas13d (UrCas13d)-crRNA complex. Two hydrated Mg2+ ions aid in stabilizing the conformation of the crRNA repeat region. Sequestration of divalent metal ions does not alter pre-crRNA processing, but abolishes target cleavage by UrCas13d. Notably, the pre-crRNA processing is executed by the HEPN-2 domain. Furthermore, both the structure and sequence of the nucleotides U(-8)-C(-1) within the repeat region are indispensable for target cleavage, and are specifically recognized by UrCas13d. Moreover, correct base pairings within two separate spacer regions (an internal and a 3'-end region) are essential for target cleavage. These findings provide a framework for the development of Cas13d into a tool for a wide range of applications.

Cartoon-block schematics in six views (download the tarball)

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