Cryo-EM structure of the mono-DdCBE bound TS substrate complex.

2025-10-01 REL PDBc INITIAL_RELEASE REPOSITORY PDBj PDBc 2024-12-08 2025-10-01 2025-10-01 2025-10-01 National Natural Science Foundation of China (NSFC) 32070170 China National Natural Science Foundation of China (NSFC) 32371272 China Ministry of Science and Technology (MoST, China) 2023ZD0500501 China Cryo-EM structure of the mono-DdCBE bound TS substrate complex. Jiangchao X Jia C Bei Y Bei Y TALE, cytosine deaminase, DdCBE, dsDNA, ND4, Mitochondrial base editor, DNA BINDING PROTEIN/DNA, DNA BINDING PROTEIN-DNA complex 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 US 85 3357 3372.e9 2025 40934924 doi:10.1016/j.molcel.2025.08.016 1097-2765 2168 MOCEFL 9ky4 FULLOVERLAP PDB 9JO8 unspecified EMDB EMD-62637 associated EM volume

The complex of TALE protein-linked deaminase with an ND51-dsDNA substrate. The complex of TALE protein-linked deaminase with an ND51-dsDNA substrate. 0 1 2 3 4

TALE protein-DddA + dsDNA

Burkholderia cenocepacia 0.110 TALE repeat protein Xanthomonas 0.070525031

The TALE repeat protein recognized 16 bp-length mitochondrial ND1 gene sequence.

1 Escherichia coli LEVO MGSSDIADLRTLGYSQQQQEKIKPKVRSTVAQHHEALVGHGFTHAHIVALSQHPAALGTVAVKYQDMIAALPEATHEAIV GVGKQWSGARALEALLTVAGELRGPPLQLDTGQLLKIAKRGGVTAVEAVHAWRNALTGAPLNLTPEQVVAIASHDGGKQA LETVQRLLPVLCQAHGLTPEQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPEQVVAIASNIGGKQALETVQRLLPVLC QAHGLTPEQVVAIASNNGGKQALETVQRLLPVLCQAHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPEQVVA IASHDGGKQALETVQRLLPVLCQAHGLTPEQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPEQVVAIASNIGGKQALE TVQRLLPVLCQAHGLTPEQVVAIASNNGGKQALETVQRLLPVLCQAHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQA HGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPEQVVAIASNNGGKQALETVQRLLPVLCQAHGLTPEQVVAIA SNGGGKQALETVQRLLPVLCQAHGLTPEQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPEQVVAIASNGGGKQALESI VAQLSRPDPALAALTNDHLVALACLGGRPALDAVKKGLG TALE repeat protein recognized single-strand DNA sequence and mitochondrial ND5.1 gene sequence. Homo sapiens 0.010649844999999998 1 (DG)(DA)(DA)(DT)(DC)(DT)(DA)(DG)(DC)(DC)(DT)(DA)(DG)(DC)(DC)(DG)(DT)(DT)(DT)(DA) (DC)(DC)(DT)(DT)(DT)(DC)(DC)(DT)(DC)(DA)(DC)(DA)(DG)(DG)(DT) DNA A complementary strand of TALE repeat protein recognized single-strand DNA sequence and mitochondrial ND5.1 gene sequence. Homo sapiens 0.010886021000000001 1 (DA)(DC)(DC)(DT)(DG)(DT)(DG)(DA)(DG)(DG)(DA)(DA)(DA)(DG)(DG)(DT)(DA)(DA)(DA)(DC) (DG)(DG)(DC)(DT)(DA)(DG)(DG)(DC)(DT)(DA)(DG)(DA)(DT)(DT)(DC) DNA Double-stranded DNA deaminase toxin A Burkholderia cenocepacia H111 0.014009717 1 Escherichia coli LEVO GSYALGPYQISAPQLPAYNGQTVGTFYYVNDAGGLESKVFISGGPTPYPNYVSAGHVAGQSALFMRDNGISEGLVFHNNP KGTCGFCVNMIETLLPENAKMTVVPPEGAIPVKRGATGETKVFIGNSNSPKSPT P0DUH5 3.5.4.- ZINC ION 6.5409e-05 1 ZN singleParticle particle 16 8.0 20.0 Tris trishydroxymethylaminomethane 150.0 Nacl sodium chloride 4.0 DTT Dithiothreitol

20 mM Tris 8.0, 150 mM NaCl, 4 mM DTT

Quantifoil R0.6/1 COPPER 300 CARBON HOLEY PLASMA CLEANING 30 OTHER ETHANE 100 281 FEI VITROBOT MARK III TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.0 2.5 130000.0 NITROGEN FEI FALCON IV (4k x 4k) 1 2340 40.0 1 3319584

initial particles from the template picker and Topaz picking

PHASE FLIPPING AND AMPLITUDE CORRECTION 3UGM C1 3.0 FSC 0.143 CUT-OFF cryoSPARC v4 343135 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_62637.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 347.14798 347.14798 347.14798 90.0 90.0 90.0 X Y Z -0.0017067058 2.0746608 0.00042488342 0.015070473 0.9642999 0.9642999 0.9642999 0.15 AUTHOR ::::EMDATABANK.org::::EMD-62637:::: The cryo-EM map of the mono-DdCBE-bound TS-substrate complex. 8e5e A 1290-1427 PDB experimental model

The initial model consisted of the D chain of current deposition complex

3UGM A 1-641 PDB experimental model

The initial model consisted of the D chain of current deposition complex

AB INITIO MODEL REAL emd_62637_msk_1.map emd_62637_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 347.14798 347.14798 347.14798 90.0 90.0 90.0 X Y Z -0.59419346 1.913414 0.00023292677 0.034227975 0.9642999 0.9642999 0.9642999 AUTHOR ::::EMDATABANK.org::::EMD-62637:::: The half map 1 of the mono-DdCBE-bound TS-substrate complex. emd_62637_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 347.14798 347.14798 347.14798 90.0 90.0 90.0 X Y Z -0.5699353 1.9351841 0.00024001626 0.03425094 0.9642999 0.9642999 0.9642999 AUTHOR ::::EMDATABANK.org::::EMD-62637:::: The half map 2 of the mono-DdCBE-bound TS-substrate complex.