SMTL ID : 9mpo.1

The cryo-EM structure of the human DNA methyltransferase DNMT3A2 and DNMT3L octamer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.271, C.274, S.276, C.291, C.294 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.271, A:C.274, A:C.291, A:C.294 ZN.2: 4 residues within 4Å: Chain A: C.314, C.317, C.336, C.339 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.314, A:C.317, A:C.336, A:C.339 ZN.3: 5 residues within 4Å: Chain A: C.326, N.328, C.331, C.360, C.363 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.326, A:C.331, A:C.360, A:C.363 ZN.7: 5 residues within 4Å: Chain D: C.271, C.274, S.276, C.291, C.294 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.271, D:C.274, D:C.291, D:C.294 ZN.8: 4 residues within 4Å: Chain D: C.314, C.317, C.336, C.339 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.314, D:C.317, D:C.336, D:C.339 ZN.9: 5 residues within 4Å: Chain D: C.326, N.328, C.331, C.360, C.363 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.326, D:C.331, D:C.360, D:C.363 ZN.11: 5 residues within 4Å: Chain E: C.271, C.274, S.276, C.291, C.294 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.271, E:C.274, E:C.291, E:C.294 ZN.12: 4 residues within 4Å: Chain E: C.314, C.317, C.336, C.339 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.314, E:C.317, E:C.336, E:C.339 ZN.13: 5 residues within 4Å: Chain E: C.326, N.328, C.331, C.360, C.363 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.326, E:C.331, E:C.360, E:C.363 ZN.15: 5 residues within 4Å: Chain F: C.271, C.274, S.276, C.291, C.294 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.271, F:C.274, F:C.291, F:C.294 ZN.16: 4 residues within 4Å: Chain F: C.314, C.317, C.336, C.339 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.314, F:C.317, F:C.336, F:C.339 ZN.17: 5 residues within 4Å: Chain F: C.326, N.328, C.331, C.360, C.363 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.326, F:C.331, F:C.360, F:C.363

6 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.4: 15 residues within 4Å: Chain A: F.417, D.418, G.419, I.420, T.422, E.441, V.442, C.443, D.463, V.464, G.484, L.507, R.668, S.669, W.670 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:I.420, A:V.442, A:D.463, A:D.463, A:V.464, A:R.668, A:W.670, A:W.670 SAH.5: 15 residues within 4Å: Chain B: F.417, D.418, G.419, I.420, T.422, E.441, V.442, C.443, D.463, V.464, G.484, L.507, R.668, S.669, W.670 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:I.420, B:T.422, B:V.442, B:D.463, B:V.464, B:R.668, B:W.670, B:W.670 SAH.6: 15 residues within 4Å: Chain C: F.417, D.418, G.419, I.420, T.422, E.441, V.442, C.443, D.463, V.464, G.484, L.507, R.668, S.669, W.670 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:I.420, C:T.422, C:V.442, C:D.463, C:V.464, C:R.668, C:W.670, C:W.670 SAH.10: 15 residues within 4Å: Chain D: F.417, D.418, G.419, I.420, T.422, E.441, V.442, C.443, D.463, V.464, G.484, L.507, R.668, S.669, W.670 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:I.420, D:V.442, D:D.463, D:V.464, D:R.668, D:W.670, D:W.670 SAH.14: 15 residues within 4Å: Chain E: F.417, D.418, G.419, I.420, T.422, E.441, V.442, C.443, D.463, V.464, G.484, L.507, R.668, S.669, W.670 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:I.420, E:V.442, E:D.463, E:V.464, E:R.668, E:W.670, E:W.670 SAH.18: 15 residues within 4Å: Chain F: F.417, D.418, G.419, I.420, T.422, E.441, V.442, C.443, D.463, V.464, G.484, L.507, R.668, S.669, W.670 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:I.420, F:T.422, F:V.442, F:D.463, F:V.464, F:R.668, F:W.670, F:W.670

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, Y. et al., Structural Insights into DNMT3A-3L-Mediated de novo DNA Methylation on Chromatin. To Be Published

Release Date

2025-10-08

Peptides

DNA (cytosine-5)-methyltransferase 3A: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

DNA (cytosine-5)-methyltransferase 3A

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