› 8j92

Electron Microscopy
2.9Å resolution

Cryo-EM structure of nucleosome containing Arabidopsis thaliana H2A.W

Released:
DOI: 10.2210/pdb8j92/pdb
PDB entry 8j92 coloured by chain, front view.
PDB entry 8j92 coloured by chain, side view.
PDB entry 8j92 coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1.
Osakabe A, Takizawa Y, Horikoshi N, Hatazawa S, Negishi L, Sato S, Berger F, Kakutani T, Kurumizaka H
OpenAccess logo Nat Commun 15 5187 (2024)
PMID: 38992002
Related structures: EMD-36085

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-246542 (preferred)
Entry contents:
4 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (6 distinct):
Histone H3.1 Chains: A, E
Molecule details ›
Chains: A, E
Length: 139 amino acids
Theoretical weight: 15.58 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: 106 amino acids
Theoretical weight: 11.72 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
Probable histone H2A.7 Chains: C, G
Molecule details ›
Chains: C, G
Length: 153 amino acids
Theoretical weight: 16.28 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9FJE8 (Residues: 1-150; Coverage: 100%)
Gene names: At5g59870, MMN10.22, MMN10_90
Sequence domains:
Histone H2B.6 Chains: D, H
Molecule details ›
Chains: D, H
Length: 153 amino acids
Theoretical weight: 16.76 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
DNA (169-MER) Chain: I
Molecule details ›
Chain: I
Length: 169 nucleotides
Theoretical weight: 51.92 KDa
DNA (169-MER) Chain: J
Molecule details ›
Chain: J
Length: 169 nucleotides
Theoretical weight: 52.42 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.9Å
Relevant EMDB volumes: EMD-36085
Expression system: Escherichia coli

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