› 7ux9

Electron Microscopy
3.2Å resolution

Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA)

Released:
DOI: 10.2210/pdb7ux9/pdb
PDB entry 7ux9 coloured by chain, front view.
PDB entry 7ux9 coloured by chain, side view.
PDB entry 7ux9 coloured by chain, top view.
Source organisms:
Primary publication:
Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation.
Lee SC, Adams DW, Ipsaro JJ, Cahn J, Lynn J, Kim HS, Berube B, Major V, Calarco JP, LeBlanc C, Bhattacharjee S, Ramu U, Grimanelli D, Jacob Y, Voigt P, Joshua-Tor L, Martienssen RA
OpenAccess logo Cell (2023)
PMID: 37643610
Related structures: EMD-26855

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-239070 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
Probable histone H2A.7 Chains: A, B
Molecule details ›
Chains: A, B
Length: 150 amino acids
Theoretical weight: 16 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9FJE8 (Residues: 1-150; Coverage: 100%)
Gene names: At5g59870, MMN10.22, MMN10_90
Sequence domains:
Histone H2B.6 Chains: C, D
Molecule details ›
Chains: C, D
Length: 150 amino acids
Theoretical weight: 16.47 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O23629 (Residues: 1-150; Coverage: 100%)
Gene names: At3g45980, F16L2.190, H2B
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H3.3 Chains: E, F
Molecule details ›
Chains: E, F
Length: 136 amino acids
Theoretical weight: 15.44 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P59169 (Residues: 1-136; Coverage: 100%)
Gene names: At4g40030, At4g40040, At5g10980, HTR4, HTR5, HTR8, T30N20_250, T5J17.200, T5J17.210, T5K6.6
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: G, H
Molecule details ›
Chains: G, H
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
ATP-dependent DNA helicase DDM1 Chain: P
Molecule details ›
Chain: P
Length: 764 amino acids
Theoretical weight: 86.76 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9XFH4 (Residues: 1-764; Coverage: 100%)
Gene names: At5g66750, CHA1, CHR1, DDM1, MSN2.14, SOM1, SOM4
Sequence domains:
DNA (sense strand) Chain: Y
Molecule details ›
Chain: Y
Length: 147 nucleotides
Theoretical weight: 45.11 KDa
DNA (antisense strand) Chain: Z
Molecule details ›
Chain: Z
Length: 147 nucleotides
Theoretical weight: 45.64 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-26855
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Role of Epigenetic Factors in Response to Stress and Establishment of Somatic Memory of Stress Exposure in Plants.
Kovalchuk I. (2023)

2 mentions without citation

Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation.
Lee et al. (2023)
1 more