SMTL ID : 8wha.1

Structure of DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-mer

Ligands

2 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.1: 6 residues within 4Å: Chain K: K.234, T.235, G.607, R.634, R.637 Ligands: ADP.2 No protein-ligand interaction detected (PLIP) BEF.3: 5 residues within 4Å: Chain L: K.234, G.607, R.634, R.637 Ligands: ADP.4 No protein-ligand interaction detected (PLIP)

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 14 residues within 4Å: Chain K: K.204, Q.207, G.231, L.232, G.233, K.234, T.235, I.236, R.272, F.273, N.609, R.637, I.638 Ligands: BEF.1 14 PLIP interactions: 14 interactions with chain K Hydrogen bonds: K:Y.206, K:Q.207, K:Q.207, K:G.231, K:L.232, K:T.235, K:T.235, K:T.235, K:I.236, K:R.272, K:N.609 Salt bridges: K:R.637, K:R.637 pi-Stacking: K:F.273 ADP.4: 13 residues within 4Å: Chain L: K.204, Q.207, G.231, L.232, G.233, K.234, T.235, I.236, R.272, N.609, R.637, I.638 Ligands: BEF.3 12 PLIP interactions: 12 interactions with chain L Hydrogen bonds: L:Q.207, L:Q.207, L:G.231, L:L.232, L:G.233, L:K.234, L:T.235, L:I.236, L:R.272, L:N.609 Salt bridges: L:R.637, L:R.637

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y. et al., Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation. Nat.Plants (2024)

Release Date

2024-04-17

Peptides

Histone H3.1: AE
Histone H4: BF
Histone H2A.6: CG
Histone H2B.6: DH
ATP-dependent DNA helicase DDM1: KL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

K
K

L
L

Histone H3.1

Histone H4

Histone H2A.6

Histone H2B.6

ATP-dependent DNA helicase DDM1

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