Crystal Structure of the Csm3-Csm4 Subcomplex in the Type III-A CRISPR-Cas Interference Complex.

Abstract Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation. The interference complex of the type III-A CRISPR–Cas system is composed of five Cas proteins (Csm1–Csm5) and a crRNA, and targets invading DNA. Here, we show that the Csm1, Csm3, and Csm4 proteins from Methanocaldococcus jannaschii form a stable subcomplex. We also report the crystal structure of the M. jannaschii Csm3–Csm4 subcomplex at 3.1 A resolution. The complex structure revealed the presence of a basic concave surface around their interface, suggesting the RNA and/or DNA binding ability of the complex. A gel retardation analysis showed that the Csm3–Csm4 complex binds single-stranded RNA in a non-sequence-specific manner. Csm4 structurally resembles Cmr3, a component of the type III-B CRISPR–Cas interference complex. Based on bioinformatics, we constructed a model structure of the Csm1–Csm4–Csm3 ternary complex, which provides insights into its role in the Csm interference complex.