8IAZ

Cryo-EM structure of the ISFba1 TnpB-reRNA-dsDNA complex

Summary for 8IAZ

• Entry DOI: 10.2210/pdb8iaz/pdb
• EMDB information: 35323
• Descriptor: Transposase, RNA (207-MER), DNA (5'-D(P*AP*CP*AP*TP*GP*GP*AP*CP*CP*AP*TP*CP*AP*GP*CP*TP*CP*CP*TP*AP*AP*TP*GP*G)-3'), ... (5 entities in total)
• Functional Keywords: rna, complex, rna binding protein/rna, rna binding protein-rna-dna complex, rna binding protein/rna/dna
• Biological source: Firmicutes bacterium AM43-11BH; More
• Total number of polymer chains: 4
• Total formula weight: 123508.38

Authors

Yin, M.,Zhou, F.,Zhu, Y.,Huang, Z. (deposition date: 2023-02-09, release date: 2024-04-17, Last modification date: 2024-05-15)

Primary citation

Ren, K.,Zhou, F.,Zhang, F.,Yin, M.,Zhu, Y.,Wang, S.,Chen, Y.,Huang, T.,Wu, Z.,He, J.,Zhang, A.,Guo, C.,Huang, Z.
Discovery and structural mechanism of DNA endonucleases guided by RAGATH-18-derived RNAs.
Cell Res., 34:370-385, 2024

PubMed Abstract: CRISPR-Cas systems and IS200/IS605 transposon-associated TnpBs have been utilized for the development of genome editing technologies. Using bioinformatics analysis and biochemical experiments, here we present a new family of RNA-guided DNA endonucleases. Our bioinformatics analysis initially identifies the stable co-occurrence of conserved RAGATH-18-derived RNAs (reRNAs) and their upstream IS607 TnpBs with an average length of 390 amino acids. IS607 TnpBs form programmable DNases through interaction with reRNAs. We discover the robust dsDNA interference activity of IS607 TnpB systems in bacteria and human cells. Further characterization of the Firmicutes bacteria IS607 TnpB system (ISFba1 TnpB) reveals that its dsDNA cleavage activity is remarkably sensitive to single mismatches between the guide and target sequences in human cells. Our findings demonstrate that a length of 20 nt in the guide sequence of reRNA achieves the highest DNA cleavage activity for ISFba1 TnpB. A cryo-EM structure of the ISFba1 TnpB effector protein bound by its cognate RAGATH-18 motif-containing reRNA and a dsDNA target reveals the mechanisms underlying reRNA recognition by ISFba1 TnpB, reRNA-guided dsDNA targeting, and the sensitivity of the ISFba1 TnpB system to base mismatches between the guide and target DNA. Collectively, this study identifies the IS607 TnpB family of compact and specific RNA-guided DNases with great potential for application in gene editing.

PubMed: 38575718
DOI: 10.1038/s41422-024-00952-1

Experimental method

ELECTRON MICROSCOPY (3 Å)