› 8kcb

Electron Microscopy
3.17Å resolution

Complex of DDM1-nucleosome(H2A) complex with DDM1 bound to SHL2

Released:
DOI: 10.2210/pdb8kcb/pdb
PDB entry 8kcb coloured by chain, front view.
PDB entry 8kcb coloured by chain, side view.
PDB entry 8kcb coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Mechanism of heterochromatin remodeling revealed by the DDM1 bound nucleosome structures.
Zhang H, Gu Z, Zeng Y, Zhang Y
Structure (2024)
PMID: 38870940
Related structures: EMD-37098

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
PDBe Complex ID:
PDB-CPX-246247 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
Histone H2B.10 Chains: C, D
Molecule details ›
Chains: C, D
Length: 145 amino acids
Theoretical weight: 15.77 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9FFC0 (Residues: 1-145; Coverage: 100%)
Gene names: At5g22880, MRN17.11
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H3.1 Chains: E, F
Molecule details ›
Chains: E, F
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: G, H
Molecule details ›
Chains: G, H
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: A, B
Molecule details ›
Chains: A, B
Length: 130 amino acids
Theoretical weight: 13.68 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli 0.1197
UniProt:
  • Canonical: Q9LD28 (Residues: 1-130; Coverage: 100%)
Gene names: At5g54640, H2A-1, MRB17.14, RAT5
Sequence domains:
ATP-dependent DNA helicase DDM1 Chain: K
Molecule details ›
Chain: K
Length: 764 amino acids
Theoretical weight: 86.76 KDa
Source organism: Arabidopsis thaliana
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9XFH4 (Residues: 1-764; Coverage: 100%)
Gene names: At5g66750, CHA1, CHR1, DDM1, MSN2.14, SOM1, SOM4
Sequence domains:
DNA (170-MER) Chain: I
Molecule details ›
Chain: I
Length: 170 nucleotides
Theoretical weight: 52.2 KDa
DNA (170-MER) Chain: J
Molecule details ›
Chain: J
Length: 170 nucleotides
Theoretical weight: 52.76 KDa

Ligands and Environments

2 bound ligands:
Ligand BEF 1 x BEF
Ligand ADP 1 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.17Å
Relevant EMDB volumes: EMD-37098
Expression systems:
  • Escherichia coli
  • Escherichia coli 0.1197
  • Spodoptera frugiperda

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