PDBe 5kgf

Electron Microscopy
4.54Å resolution

Structural model of 53BP1 bound to a ubiquitylated and methylated nucleosome, at 4.5 A resolution

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 14-mer (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (8 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: 11.44 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: 14.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0C0S8 (Residues: 1-130; Coverage: 100%)
Gene names: H2AFC, H2AFD, H2AFI, H2AFN, H2AFP, HIST1H2AG, HIST1H2AI, HIST1H2AK, HIST1H2AL, HIST1H2AM
Sequence domains:
Histone H2B type 1-C/E/F/G/I Chains: D, H
Molecule details ›
Chains: D, H
Length: 126 amino acids
Theoretical weight: 13.94 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62807 (Residues: 1-126; Coverage: 100%)
Gene names: H2BFA, H2BFG, H2BFH, H2BFK, H2BFL, HIST1H2BC, HIST1H2BE, HIST1H2BF, HIST1H2BG, HIST1H2BI
Sequence domains: Core histone H2A/H2B/H3/H4
TP53-binding protein 1 Chains: K, L
Molecule details ›
Chains: K, L
Length: 21 amino acids
Theoretical weight: 2.38 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q12888 (Residues: 1611-1631; Coverage: 1%)
Gene name: TP53BP1
Ubiquitin Chains: M, O
Molecule details ›
Chains: M, 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
DNA (145-MER) Chain: I
Molecule details ›
Chain: I
Length: 145 nucleotides
Theoretical weight: 44.52 KDa
DNA (145-MER) Chain: J
Molecule details ›
Chain: J
Length: 145 nucleotides
Theoretical weight: 44.99 KDa

Ligands and Environments

No bound ligands

1 modified residue:

Experiments and Validation Details

Entry percentile scores
Resolution: 4.54Å
Relevant EMDB volumes: EMD-8246
Expression system: Escherichia coli