Molecular cellDec 4, 2018

How Type III-A CRISPR-Cas Csm Complexes Form, Cut RNA in Patterns, Control DNA Cutting, and Prevent Self-Attack

CRISPR Gene Editing Weekly Brief ↗PubMed ↗DOI ↗

Updated Mar 25, 2026

Abstract

Cryo-EM structures reveal 3.1 Å resolution details of the Csm complex involved in RNA targeting.

Type III CRISPR-Cas systems provide immunity against foreign RNA and DNA through specific RNA degradation mechanisms.
The structure of the crRNA 5'-repeat tag explains how target cleavage sites are defined using a 5'-ruler mechanism.
Positions -2 to -5 within the crRNA 5'-repeat act as sensors to prevent autoimmunity.
Periodic kinks introduced by Csm3 thumb elements in the crRNA-target RNA duplex help achieve cleavage with 6-nucleotide periodicity.
Autoinhibitory conformations of key Glu residues in Csm1 suggest a regulatory role in DNase activity.
Mutational studies support insights into the assembly of the Csm complex and the mechanisms of RNA targeting.

Simplified

Type ΙΙΙ CRISPR-Cas systems provide robust immunity against foreign RNA and DNA by sequence-specific RNase and target RNA-activated sequence-nonspecific DNase and RNase activities. We report on cryo-EM structures of Thermococcus onnurineus Csmbinary, Csm-target RNA and Csm-target RNAternary complexes in the 3.1 Å range. The topological features of the crRNA 5'-repeat tag explains the 5'-ruler mechanism for defining target cleavage sites, with accessibility of positions -2 to -5 within the 5'-repeat serving as sensors for avoidance of autoimmunity. The Csm3 thumb elements introduce periodic kinks in the crRNA-target RNA duplex, facilitating cleavage of the target RNA with 6-nt periodicity. Key Glu residues within a Csm1 loop segment of Csmadopt a proposed autoinhibitory conformation suggestive of DNase activity regulation. These structural findings, complemented by mutational studies of key intermolecular contacts, provide insights into Csmcomplex assembly, mechanisms underlying RNA targeting and site-specific periodic cleavage, regulation of DNase cleavage activity, and autoimmunity suppression. crRNA crRNA crRNA anti-tag crRNA crRNA

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Funding

Competing interests

DECLARATION OF INTERESTS. L.A.M. is a cofounder and Scientific Advisory Board member of Intellia Therapeutics and Eligo Biosciences; all of which develop CRISPR-based technologies.

PubMed

How Type III-A CRISPR-Cas Csm Complexes Form, Cut RNA in Patterns, Control DNA Cutting, and Prevent Self-Attack

Abstract

Full Text

Funding

Competing interests

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