SMTL ID : 9mp0.1

The cryo-EM structure of the human DNA methyltransferases DNMT3A2 and DNMT3L dodecamer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-8-2-mer

Ligands

30 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: 5 residues within 4Å: Chain A: C.314, I.316, 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.5: 5 residues within 4Å: Chain B: C.271, C.274, S.276, C.291, C.294 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.271, B:C.274, B:C.291, B:C.294 ZN.6: 4 residues within 4Å: Chain B: C.314, C.317, C.336, C.339 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.314, B:C.317, B:C.336, B:C.339 ZN.7: 5 residues within 4Å: Chain B: C.326, N.328, C.331, C.360, C.363 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.326, B:C.331, B:C.360, B:C.363 ZN.9: 5 residues within 4Å: Chain C: C.271, C.274, S.276, C.291, C.294 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.271, C:C.274, C:C.291, C:C.294 ZN.10: 5 residues within 4Å: Chain C: C.314, I.316, C.317, C.336, C.339 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.314, C:C.317, C:C.336, C:C.339 ZN.11: 4 residues within 4Å: Chain C: C.326, C.331, C.360, C.363 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.326, C:C.331, C:C.360, C:C.363 ZN.13: 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.14: 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.15: 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.17: 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.18: 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.19: 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.21: 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.22: 5 residues within 4Å: Chain F: C.314, I.316, 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.23: 4 residues within 4Å: Chain F: C.326, 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 ZN.25: 5 residues within 4Å: Chain G: C.271, C.274, S.276, C.291, C.294 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.271, G:C.274, G:C.291, G:C.294 ZN.26: 4 residues within 4Å: Chain G: C.314, C.317, C.336, C.339 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.314, G:C.317, G:C.336, G:C.339 ZN.27: 5 residues within 4Å: Chain G: C.326, N.328, C.331, C.360, C.363 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.326, G:C.331, G:C.360, G:C.363 ZN.29: 5 residues within 4Å: Chain H: C.271, C.274, S.276, C.291, C.294 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.271, H:C.274, H:C.291, H:C.294 ZN.30: 5 residues within 4Å: Chain H: C.314, I.316, C.317, C.336, C.339 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.314, H:C.317, H:C.336, H:C.339 ZN.31: 5 residues within 4Å: Chain H: C.326, N.328, C.331, C.360, C.363 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.326, H:C.331, H:C.360, H:C.363 ZN.33: 4 residues within 4Å: Chain I: C.53, C.56, C.73, C.76 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.53, I:C.56, I:C.73, I:C.76 ZN.34: 4 residues within 4Å: Chain I: C.96, C.99, C.118, C.121 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.96, I:C.99, I:C.118, I:C.121 ZN.35: 4 residues within 4Å: Chain I: C.108, C.113, C.142, C.145 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.108, I:C.113, I:C.142, I:C.145 ZN.36: 4 residues within 4Å: Chain J: C.53, C.56, C.73, C.76 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.53, J:C.56, J:C.73, J:C.76 ZN.37: 4 residues within 4Å: Chain J: C.96, C.99, C.118, C.121 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.96, J:C.99, J:C.118, J:C.121 ZN.38: 4 residues within 4Å: Chain J: C.108, C.113, C.142, C.145 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.108, J:C.113, J:C.142, J:C.145

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

SAH.4: 16 residues within 4Å: Chain A: F.417, D.418, G.419, I.420, T.422, S.440, E.441, V.442, D.463, V.464, G.484, P.486, L.507, R.668, S.669, W.670 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.420, A:T.422, A:V.442, A:D.463, A:W.670, A:W.670 SAH.8: 16 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, P.486, L.507, R.668, S.669, W.670 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.420, B:V.442, B:D.463, B:W.670, B:W.670 SAH.12: 16 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, P.486, L.507, R.668, S.669, W.670 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:I.420, C:V.442, C:D.463, C:V.464, C:W.670, C:W.670 SAH.16: 17 residues within 4Å: Chain D: F.417, D.418, G.419, I.420, T.422, S.440, E.441, V.442, C.443, D.463, V.464, G.484, P.486, L.507, R.668, S.669, W.670 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:I.420, D:T.422, D:V.442, D:D.463, D:V.464, D:W.670, D:W.670 SAH.20: 17 residues within 4Å: Chain E: F.417, D.418, G.419, I.420, T.422, S.440, E.441, V.442, C.443, D.463, V.464, G.484, P.486, L.507, R.668, S.669, W.670 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:I.420, E:T.422, E:V.442, E:D.463, E:V.464, E:W.670, E:W.670 SAH.24: 16 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, P.486, L.507, R.668, S.669, W.670 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:I.420, F:T.422, F:V.442, F:D.463, F:V.464, F:W.670, F:W.670 SAH.28: 17 residues within 4Å: Chain G: F.417, D.418, G.419, I.420, T.422, E.441, V.442, C.443, D.463, V.464, G.484, S.485, P.486, L.507, R.668, S.669, W.670 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:I.420, G:V.442, G:D.463, G:R.668, G:W.670, G:W.670 SAH.32: 16 residues within 4Å: Chain H: F.417, D.418, G.419, I.420, T.422, S.440, E.441, V.442, D.463, V.464, G.484, P.486, L.507, R.668, S.669, W.670 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:I.420, H:T.422, H:V.442, H:D.463, H:V.464, H:W.670, H:W.670

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, Y. et al., Mechanisms of DNMT3A-3L-mediated de novo DNA methylation on chromatin. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-10-08

Peptides

DNA (cytosine-5)-methyltransferase 3A: ABCDEFGH
DNA (cytosine-5)-methyltransferase 3-like: IJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
M

C
N

D
O

E
R

F
S

G
T

H
U

I
P

J
Q

DNA (cytosine-5)-methyltransferase 3A

DNA (cytosine-5)-methyltransferase 3-like

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