9LD0

Inactivate TOD6 with CC DNA substrate

Summary for 9LD0

• Entry DOI: 10.2210/pdb9ld0/pdb
• Related: 9LCX
• EMDB information: 62998
• Descriptor: CC DNA substrate forward strand, CC DNA substrate reverse strand, Inactivate TOD6, ... (4 entities in total)
• Functional Keywords: de novo design, dna-binding tale domain, deaminase(ddd_ss), orienting domain, de novo protein
• Biological source: synthetic construct; More
• Total number of polymer chains: 3
• Total formula weight: 112478.24

Authors

Lv, X.C.,Mi, L.,Lu, P.L. (deposition date: 2025-01-05, release date: 2025-11-19, Last modification date: 2025-12-31)

Primary citation

Mi, L.,Li, Y.X.,Lv, X.,Wan, Z.L.,Liu, X.,Zhang, K.,Li, H.,Yao, Y.,Zhang, L.,Xu, Z.,Zhuang, X.,Ji, K.,Jiang, M.,Wang, Y.,Lu, P.
Computational design of a high-precision mitochondrial DNA cytosine base editor.
Nat.Struct.Mol.Biol., 32:2575-2586, 2025

PubMed Abstract: Bystander editing remains a major limitation of current base editors, hindering their precision and therapeutic potential. Here, we present a de novo protein design strategy that creates a structurally rigid interface between a DNA-binding TALE domain and a cytosine deaminase, forming a unified editing module termed TALE-oriented deaminase (TOD). Cryo-EM analysis of TOD-DNA complexes confirms that this precise spatial architecture tightly restricts the deaminase activity window, thereby minimizing unwanted deamination. To further enhance editing specificity, we develop a split version, termed DdCBE-TOD, which virtually eliminates off-target editing. As a proof of concept, we apply DdCBE-TOD to generate a mitochondrial disease mouse model and to correct a pathogenic mutation associated with MERRF syndrome in patient-derived cells, achieving single-nucleotide precision. This work introduces a generalizable and computationally guided approach for ultra-precise base editing, offering a promising platform for both mechanistic studies and therapeutic correction of single-nucleotide mutations.

PubMed: 41249818
DOI: 10.1038/s41594-025-01714-2

Experimental method

ELECTRON MICROSCOPY (3.17 Å)