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

Electron Microscopy
4.54Å resolution
PDB entry 5kgf coloured by chain, front view.
PDB entry 5kgf coloured by chain, side view.
PDB entry 5kgf coloured by chain, top view.
Source organisms:
Assembly composition:
hetero tetradecamer (preferred)
Entry contents: 6 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero tetradecamer
Accessible surface area: 85625.88 Å2
Buried surface area: 64291.62 Å2
Dissociation area: 2,940.8 Å2
Dissociation energy (ΔGdiss): -10.02 kcal/mol
Dissociation entropy (TΔSdiss): 41.84 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-118946

Macromolecules

Histone H3.2
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%)
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
Histone H3.2 in PDB entry 5kgf, assembly 1, front view.
Histone H3.2 in PDB entry 5kgf, assembly 1, side view.
Histone H3.2 in PDB entry 5kgf, assembly 1, top view.
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Histone H4
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%)
Pfam: Centromere kinetochore component CENP-T histone fold
InterPro:
Histone H4 in PDB entry 5kgf, assembly 1, front view.
Histone H4 in PDB entry 5kgf, assembly 1, side view.
Histone H4 in PDB entry 5kgf, assembly 1, top view.
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Histone H2A type 1
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: H2AC11, H2AC13, H2AC15, H2AC16, H2AC17, H2AFC, H2AFD, H2AFI, H2AFN, H2AFP, HIST1H2AG, HIST1H2AI, HIST1H2AK, HIST1H2AL, HIST1H2AM
Pfam:
InterPro:
Histone H2A type 1 in PDB entry 5kgf, assembly 1, front view.
Histone H2A type 1 in PDB entry 5kgf, assembly 1, side view.
Histone H2A type 1 in PDB entry 5kgf, assembly 1, top view.
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Histone H2B type 1-C/E/F/G/I
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: H2BC10, H2BC4, H2BC6, H2BC7, H2BC8, H2BFA, H2BFG, H2BFH, H2BFK, H2BFL, HIST1H2BC, HIST1H2BE, HIST1H2BF, HIST1H2BG, HIST1H2BI
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
Histone H2B type 1-C/E/F/G/I in PDB entry 5kgf, assembly 1, front view.
Histone H2B type 1-C/E/F/G/I in PDB entry 5kgf, assembly 1, side view.
Histone H2B type 1-C/E/F/G/I in PDB entry 5kgf, assembly 1, top view.
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TP53-binding protein 1
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
TP53-binding protein 1 in PDB entry 5kgf, assembly 1, front view.
TP53-binding protein 1 in PDB entry 5kgf, assembly 1, side view.
TP53-binding protein 1 in PDB entry 5kgf, assembly 1, top view.
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Ubiquitin
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
Pfam: Ubiquitin family
InterPro:
Ubiquitin in PDB entry 5kgf, assembly 1, front view.
Ubiquitin in PDB entry 5kgf, assembly 1, side view.
Ubiquitin in PDB entry 5kgf, assembly 1, top view.
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DNA chain I
Name: DNA (145-MER)
Representative chains: I
Length: 145 nucleotides
Theoretical weight: 44.52 KDa
DNA (145-MER) in PDB entry 5kgf, assembly 1, front view.
DNA (145-MER) in PDB entry 5kgf, assembly 1, side view.
DNA (145-MER) in PDB entry 5kgf, assembly 1, top view.
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DNA chain J
Name: DNA (145-MER)
Representative chains: J
Length: 145 nucleotides
Theoretical weight: 44.99 KDa
DNA (145-MER) in PDB entry 5kgf, assembly 1, front view.
DNA (145-MER) in PDB entry 5kgf, assembly 1, side view.
DNA (145-MER) in PDB entry 5kgf, assembly 1, top view.
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