PDBe 6ftx

Electron Microscopy
4.5Å resolution

Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 13-mer (preferred)
Entry contents:
7 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (9 distinct):
Histone H3 Chain: A
Molecule details ›
Chain: A
Length: 97 amino acids
Theoretical weight: 11.43 KDa
Source organism: Petromyzon marinus
Expression system: Escherichia coli
UniProt:
  • Canonical: S4RAZ3 (Residues: 62-158; Coverage: 61%)
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 Chains: D, H
Molecule details ›
Chains: D, H
Length: 126 amino acids
Theoretical weight: 13.94 KDa
Source organism: Xenopus tropicalis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q28D68 (Residues: 1-126; Coverage: 100%)
Gene names: LOC108648866, TGas058p09.1-001, XENTR_v90029327mg, XENTR_v90029353mg, hist2h2bf
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H3.3C Chain: E
Molecule details ›
Chain: E
Length: 110 amino acids
Theoretical weight: 12.33 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02302 (Residues: 30-136; Coverage: 79%)
Gene name: h3f3c
Ubiquitin Chains: N, O
Molecule details ›
Chains: N, O
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family
Chromo domain-containing protein 1 Chain: W
Molecule details ›
Chain: W
Length: 878 amino acids
Theoretical weight: 102.15 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P32657 (Residues: 175-1269; Coverage: 60%)
Gene names: CHD1, SYGP-ORF4, YER164W
Sequence domains:
DNA (159-MER) Chain: I
Molecule details ›
Chain: I
Length: 159 nucleotides
Theoretical weight: 48.79 KDa
DNA (160-MER) Chain: J
Molecule details ›
Chain: J
Length: 160 nucleotides
Theoretical weight: 49.68 KDa

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.5Å
Relevant EMDB volumes: EMD-4318
Expression system: Escherichia coli