9KY4
Cryo-EM structure of the mono-DdCBE bound TS substrate complex.
Summary for 9KY4
| Entry DOI | 10.2210/pdb9ky4/pdb |
| Related | 9JO8 |
| EMDB information | 62637 |
| Descriptor | TALE repeat protein, TALE repeat protein recognized single-strand DNA sequence and mitochondrial ND5.1 gene sequence., A complementary strand of TALE repeat protein recognized single-strand DNA sequence and mitochondrial ND5.1 gene sequence., ... (5 entities in total) |
| Functional Keywords | tale, cytosine deaminase, ddcbe, dsdna, nd4, mitochondrial base editor, dna binding protein/dna, dna binding protein-dna complex |
| Biological source | Xanthomonas More |
| Total number of polymer chains | 4 |
| Total formula weight | 106136.02 |
| Authors | |
| Primary citation | Xiang, J.,Xu, W.,Wu, J.,Luo, Y.,Liu, C.,Hou, Y.,Chen, J.,Yang, B. Structural insights into DdCBE in action enable high-precision mitochondrial DNA editing. Mol.Cell, 85:3357-3372.e9, 2025 Cited by PubMed Abstract: DddA-derived cytosine base editor (DdCBE) couples transcription activator-like effector (TALE) arrays and the double-stranded DNA (dsDNA)-specific cytidine deaminase DddA to target mitochondrial DNA (mtDNA) for editing. However, structures of DdCBE in action are unavailable, impeding its mechanistic-based optimization for high-precision-demanding therapeutic applications. Here, we determined the cryo-electron microscopy (cryo-EM) structures of DdCBE targeting two native mitochondrial gene loci and combined editing data from systematically designed spacers to develop WinPred, a model that can predict DdCBE's editing outcome and guide its design to achieve high-precision editing. Furthermore, structure-guided engineering of DddA narrowed the editing window of DdCBE to 2-3 nt while minimizing its off-target (OT) editing to near-background levels, thereby generating accurate DdCBE (aDdCBE). Using aDdCBE, we precisely introduced a Leber hereditary optic neuropathy (LHON)-disease-related mutation into mtDNA and faithfully recapitulated the pathogenic conditions without interference from unintended bystander or OT mutations. Our work provides a mechanistic understanding of DdCBE and establishes WinPred and aDdCBE as useful tools for faithfully modeling or correcting disease-related mtDNA mutations. PubMed: 40934924DOI: 10.1016/j.molcel.2025.08.016 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3 Å) |
Structure validation
Download full validation report
