› 8wha

Electron Microscopy
4.05Å resolution

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

Released:
DOI: 10.2210/pdb8wha/pdb
PDB entry 8wha coloured by chain, front view.
PDB entry 8wha coloured by chain, side view.
PDB entry 8wha coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation.
Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J
Nat Plants 10 374-380 (2024)
PMID: 38413824
Related structures: EMD-37537

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-243088 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
Histone H3.1 Chains: A, E
Molecule details ›
Chains: A, E
Length: 136 amino acids
Theoretical weight: 15.3 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: P59226 (Residues: 1-136; Coverage: 100%)
Gene names: At1g09200, At3g27360, At5g10390, At5g10400, At5g65360, F12B17_250, F12B17_260, HTR1, HTR13, HTR2, HTR3, HTR9, K1G2.8, MNA5.9, T12M4.9
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 103 amino acids
Theoretical weight: 11.44 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: P59259 (Residues: 1-103; Coverage: 100%)
Gene names: At1g07660, At1g07820, At2g28740, At3g45930, At3g46320, At3g53730, At5g59690, At5g59970, F16L2_140, F18L15.40, F24B9.25, F24B9.8, F5K20_30, F8N16.2, MMN10.22, MTH12.10, T11P11.4
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A.6 Chains: C, G
Molecule details ›
Chains: C, G
Length: 130 amino acids
Theoretical weight: 13.68 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9LD28 (Residues: 1-130; Coverage: 100%)
Gene names: At5g54640, H2A-1, MRB17.14, RAT5
Sequence domains:
Histone H2B.6 Chains: D, H
Molecule details ›
Chains: D, H
Length: 150 amino acids
Theoretical weight: 16.47 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: O23629 (Residues: 1-150; Coverage: 100%)
Gene names: At3g45980, F16L2.190, H2B
Sequence domains: Core histone H2A/H2B/H3/H4
ATP-dependent DNA helicase DDM1 Chains: K, L
Molecule details ›
Chains: K, L
Length: 765 amino acids
Theoretical weight: 86.84 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9XFH4 (Residues: 1-764; Coverage: 100%)
Gene names: At5g66750, CHA1, CHR1, DDM1, MSN2.14, SOM1, SOM4
Sequence domains:
DNA (sense strand) Chain: I
Molecule details ›
Chain: I
Length: 147 nucleotides
Theoretical weight: 45.12 KDa
DNA (antisense strand) Chain: J
Molecule details ›
Chain: J
Length: 147 nucleotides
Theoretical weight: 45.63 KDa

Ligands and Environments

2 bound ligands:
Ligand BEF 2 x BEF
Ligand ADP 2 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.05Å
Relevant EMDB volumes: EMD-37537
Expression system: Escherichia coli

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Citations

1 citations in other articles

Blasting away a fungal pathogen.
Taglialegna A. (2024)