› 7xnp

Electron Microscopy
2.9Å resolution

Structure of nucleosome-AAG complex (A-55I, post-catalytic state)

Released:
DOI: 10.2210/pdb7xnp/pdb
PDB entry 7xnp coloured by chain, front view.
PDB entry 7xnp coloured by chain, side view.
PDB entry 7xnp coloured by chain, top view.
Source organism: Xenopus laevis
Primary publication:
Structural and mechanistic insights into the DNA glycosylase AAG-mediated base excision in nucleosome.
Zheng L, Tsai B, Gao N
OpenAccess logo Cell Discov 9 62 (2023)
PMID: 37339965
Related structures: EMD-33322

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-215065 (preferred)
Entry contents:
4 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (6 distinct):
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 136 amino acids
Theoretical weight: 15.42 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 1-136; Coverage: 100%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1 Chains: C, G
Molecule details ›
Chains: C, G
Length: 130 amino acids
Theoretical weight: 14.09 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 1-130; Coverage: 100%)
Sequence domains:
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 126 amino acids
Theoretical weight: 13.97 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 1-126; Coverage: 100%)
Sequence domains: Core histone H2A/H2B/H3/H4
DNA (152-MER) Chain: I
Molecule details ›
Chain: I
Length: 152 nucleotides
Theoretical weight: 47.17 KDa
DNA (152-MER) Chain: J
Molecule details ›
Chain: J
Length: 152 nucleotides
Theoretical weight: 46.67 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.9Å
Relevant EMDB volumes: EMD-33322
Expression system: Escherichia coli

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