[English] 日本語
Yorodumi
- EMDB-62997: Inactivate TOD6 with GC DNA substrate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62997
TitleInactivate TOD6 with GC DNA substrate
Map data
Sample
  • Complex: Inactivate TOD6 with GC DNA substrate
    • Protein or peptide: Inactivate TOD6
    • DNA: GC DNA substrate forward strand
    • DNA: GC DNA substrate reverse strand
  • Ligand: ZINC ION
KeywordsDe novo design / DNA-binding TALE domain / deaminase(Ddd_Ss) / orienting domain / DE NOVO PROTEIN
Biological speciesXanthomonas (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsLv XC / Mi L / Lu PL
Funding support China, 2 items
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, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_62997.png

Downloads & links

-
Map

FileDownload / File: emd_62997.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 275.789 Å		1.08 Å/pix.
x 256 pix.
= 275.789 Å		1.08 Å/pix.
x 256 pix.
= 275.789 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0773 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-8.660316 - 11.362415
Average (Standard dev.)0.00062420673 (±0.15551154)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 275.7888 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_62997_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62997_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Inactivate TOD6 with GC DNA substrate

EntireName: Inactivate TOD6 with GC DNA substrate
Components
  • Complex: Inactivate TOD6 with GC DNA substrate
    • Protein or peptide: Inactivate TOD6
    • DNA: GC DNA substrate forward strand
    • DNA: GC DNA substrate reverse strand
  • Ligand: ZINC ION

-
Supramolecule #1: Inactivate TOD6 with GC DNA substrate

SupramoleculeName: Inactivate TOD6 with GC DNA substrate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Xanthomonas (bacteria)

-
Macromolecule #1: Inactivate TOD6

MacromoleculeName: Inactivate TOD6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xanthomonas (bacteria)
Molecular weightTheoretical: 93.232461 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MASSHHHHHH HHSGASVDLR TLGYSQQQQE KIKPKVRSTV AQHHEALVGH GFTHAHIVAL SQHPAALGTV AVKYQDMIAA LPEATHEAI VGVGKQWSGA RALEALLTVA GELRGPPLQL DTGQLLKIAK RGGVTAVEAV HAWRNALTGA PLNLTPEQVV A IASHDGGK ...String:
MASSHHHHHH HHSGASVDLR TLGYSQQQQE KIKPKVRSTV AQHHEALVGH GFTHAHIVAL SQHPAALGTV AVKYQDMIAA LPEATHEAI VGVGKQWSGA RALEALLTVA GELRGPPLQL DTGQLLKIAK RGGVTAVEAV HAWRNALTGA PLNLTPEQVV A IASHDGGK QALETVQRLL PVLCQAHGLT PEQVVAIASN IGGKQALETV QRLLPVLCQA HGLTPEQVVA IASNNGGKQA LE TVQRLLP VLCQAHGLTP EQVVAIASNN GGKQALETVQ RLLPVLCQAH GLTPEQVVAI ASNIGGKQAL ETVQRLLPVL CQA HGLTPE QVVAIASNGG GKQALETVQR LLPVLCQAHG LTPEQVVAIA SNIGGKQALE TVQRLLPVLC QAHGLTPEQV VAIA SHDGG KQALETVQRL LPVLCQAHGL TPEQVVAIAS NGGGKQALET VQRLLPVLCQ AHGLTPEQVV AIASHDGGKQ ALETV QRLL PVLCQAHGLT PEQVVAIASH DGGKQALETV QRLLPVLCQA HGLTPEQVVA IASNGGGKQA LETVQRLLPV LCQAHG LTP EQVVAIASHD GGKQALETVQ RLLPVLCQAH GLTPEQVVAI ASNIGGKQAL ETVQRLLPVL CQAHGLTPEQ VVAIASN IG GKQALETVQR LLPVLCQAHG LTPEQVVAIA SNGGGRPALE ALHAVLTDGP EEAKYEALMR LGGALAIRIS DNSEKQIN T AINLIKNHAK SKGVELSEED IKKVEKILKE NPGVVLLLTP SGKIHVFPSI SWSLPEYDGT TTHGVLVLDD GTQIGFTSG NGDPRYTNYR NNGHVAQKSA LYMRENNISN ATVYHNNTNG TCGYCNTMTA TFLPEGATLT VVPPENAVAN NSRAIDYVKT YTGTS

-
Macromolecule #2: GC DNA substrate forward strand

MacromoleculeName: GC DNA substrate forward strand / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.473098 KDa
SequenceString:
(DT)(DG)(DT)(DC)(DA)(DG)(DG)(DA)(DT)(DA) (DC)(DT)(DC)(DC)(DT)(DC)(DA)(DA)(DT)(DC) (DT)(DA)(DC)(DC)(DG)(DG)(DC)(DC)(DG) (DA)(DG)

-
Macromolecule #3: GC DNA substrate reverse strand

MacromoleculeName: GC DNA substrate reverse strand / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.593171 KDa
SequenceString:
(DC)(DT)(DC)(DG)(DG)(DC)(DC)(DG)(DG)(DT) (DA)(DG)(DA)(DT)(DT)(DG)(DA)(DG)(DG)(DA) (DG)(DT)(DA)(DT)(DC)(DC)(DT)(DG)(DA) (DC)(DA)

-
Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration6 mg/mL
BufferpH: 6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3v6t

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.2.1) / Number images used: 964225
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9lcz:
Inactivate TOD6 with GC DNA substrate

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more