9VTQ

Target DNA-bound type I-F3 TniQ-Cascade of Vibrio parahaemolyticus in full R-loop state 1

Summary for 9VTQ

• Entry DOI: 10.2210/pdb9vtq/pdb
• EMDB information: 65339
• Descriptor: crRNA from Vibrio parahaemolyticus, Target strand DNA, Non-target strand DNA, ... (8 entities in total)
• Functional Keywords: crispr-associated transposon, dna binding protein
• Biological source: Vibrio parahaemolyticus RIMD 2210633; More
• Total number of polymer chains: 13
• Total formula weight: 508519.96

Authors

Ishihara, K.,Numata, T. (deposition date: 2025-07-11, release date: 2026-02-11)

Primary citation

Ishihara, K.,Matsumoto, S.,Gerle, C.,Gopalasingam, C.C.,Shigematsu, H.,Shirai, T.,Numata, T.
Sequential structural rearrangements at the PAM-distal site of a type I-F3 CRISPR-Cas effector enabling RNA-guided DNA transposition.
Nucleic Acids Res., 54:-, 2026

PubMed Abstract: Some prokaryotes carry CRISPR-associated transposons (CASTs), Tn7-like elements that incorporate genes encoding CRISPR-Cas effectors. CAST insertion is directed by CRISPR-Cas effectors through RNA-guided DNA binding and interactions with transposition-associated proteins. Although efficient sequence-specific DNA integration requires both precise target DNA recognition and coordinated interactions between effectors and transposition-associated proteins, the underlying mechanism remains elusive. Here, we determined three cryo-EM structures of target DNA-bound type I-F3 TniQ-Cascade from Vibrio parahaemolyticus, revealing how Cas8/5 recognizes the protospacer adjacent motif (PAM) and identifying a key residue responsible for the cytidine preference at position -2 of the PAM. We revealed mismatch tolerance at the PAM-proximal site. Structural analyses showed that correct base pairing at the PAM-distal site correlates with conformational changes in the Cas8/5 helical bundle and TniQ, bending the DNA to guide its downstream region toward the transposition machinery. Together, these dynamic rearrangements at the PAM-distal region provide insights into the licensing mechanism of type I-F3 CAST transposition and highlight its potential for genome engineering applications.

PubMed: 41495894
DOI: 10.1093/nar/gkaf1415

Experimental method

ELECTRON MICROSCOPY (2.84 Å)