SNAP output for PDB entry 8yha [SNAP web server]

PDB-id

8yha; SNAP-derived features in text and JSON formats; DNAproDB

Class

RNA binding protein-DNA-RNA

Method

cryo-EM (3.4 Å)

Summary

Type i-ehnh cascade-ssDNA complex

Reference

Zhang C, Chen F, Wang F, Xu H, Xue J, Li Z (2024): "Mechanisms for HNH-mediated target DNA cleavage in type I CRISPR-Cas systems." Mol.Cell, 84, 3141. doi: 10.1016/j.molcel.2024.06.033.

Abstract

The metagenome-derived type I-E and type I-F variant CRISPR-associated complex for antiviral defense (Cascade) complexes, fused with HNH domains, precisely cleave target DNA, representing recently identified genome editing tools. However, the underlying working mechanisms remain unknown. Here, structures of type I-F_HNH and I-E_HNH Cascade complexes at different states are reported. In type I-F_HNH Cascade, Cas8f_HNH loosely attaches to Cascade head and is adjacent to the 5' end of the target single-stranded DNA (ssDNA). Formation of the full R-loop drives the Cascade head to move outward, allowing Cas8f_HNH to detach and rotate ∼150° to accommodate target ssDNA for cleavage. In type I-E_HNH Cascade, Cas5e_HNH domain is adjacent to the 5' end of the target ssDNA. Full crRNA-target pairing drives the lift of the Cascade head, widening the substrate channel for target ssDNA entrance. Altogether, these analyses into both complexes revealed that crRNA-guided positioning of target DNA and target DNA-induced HNH unlocking are two key factors for their site-specific cleavage of target DNA.