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- PDB-9lcz: Inactivate TOD6 with GC DNA substrate -

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Basic information

Entry
Database: PDB / ID: 9lcz
TitleInactivate TOD6 with GC DNA substrate
Components
  • GC DNA substrate forward strand
  • GC DNA substrate reverse strand
  • Inactivate TOD6
KeywordsDE NOVO PROTEIN / De novo design / DNA-binding TALE domain / deaminase(Ddd_Ss) / orienting domain
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesXanthomonas (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsLv, X.C. / Mi, L. / Lu, P.L.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0909200 China
Ministry of Education (MoE, China)2024M762947 China
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Computational design of a high-precision mitochondrial DNA cytosine base editor.
Authors: Li Mi / Yu-Xuan Li / Xinchen Lv / Zi-Li Wan / Xu Liu / Kairan Zhang / Huican Li / Yue Yao / Leping Zhang / Zhe Xu / Xingyu Zhuang / Kunqian Ji / Min Jiang / Yangming Wang / Peilong Lu /
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 ...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.
History
DepositionJan 5, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inactivate TOD6
B: GC DNA substrate forward strand
C: GC DNA substrate reverse strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,3644
Polymers112,2993
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Inactivate TOD6


Mass: 93232.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: DNA chain GC DNA substrate forward strand


Mass: 9473.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain GC DNA substrate reverse strand


Mass: 9593.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Inactivate TOD6 with GC DNA substrate / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Xanthomonas (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 6
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.2.1particle selection
2PHENIX1.21.2_5419:model refinement
13cryoSPARCv4.2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 964225 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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