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Structure of the 4_601_157 tetranucleosome (P1 form)

X-ray diffraction
5.774Å resolution
PDB entry 5oy7 coloured by chain, front view.
PDB entry 5oy7 coloured by chain, side view.
PDB entry 5oy7 coloured by chain, top view.
Source organism: Xenopus laevis
Assembly composition:
hetero 34-mer (preferred)
Entry contents: 4 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Nucleosome, Histone and DNA
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Multimeric state: hetero 34-mer
Accessible surface area: 298078.68 Å2
Buried surface area: 232793.12 Å2
Dissociation area: 4,322.73 Å2
Dissociation energy (ΔGdiss): 69.07 kcal/mol
Dissociation entropy (TΔSdiss): 12.99 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-119120

Macromolecules

Histone H2B 1.1
Chains: D, H, L, P, T, X, b, f
Length: 126 amino acids
Theoretical weight: 13.98 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 1-126; Coverage: 100%)
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
Histone H2B 1.1 in PDB entry 5oy7, assembly 1, front view.
Histone H2B 1.1 in PDB entry 5oy7, assembly 1, side view.
Histone H2B 1.1 in PDB entry 5oy7, assembly 1, top view.
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Histone H3.2
Chains: A, E, I, M, Q, U, Y, c
Length: 135 amino acids
Theoretical weight: 15.3 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 2-136; Coverage: 99%)
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
Histone H3.2 in PDB entry 5oy7, assembly 1, front view.
Histone H3.2 in PDB entry 5oy7, assembly 1, side view.
Histone H3.2 in PDB entry 5oy7, assembly 1, top view.
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Histone H4
Chains: B, F, J, N, R, V, Z, d
Length: 102 amino acids
Theoretical weight: 11.26 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 2-103; Coverage: 99%)
Pfam: Centromere kinetochore component CENP-T histone fold
InterPro:
Histone H4 in PDB entry 5oy7, assembly 1, front view.
Histone H4 in PDB entry 5oy7, assembly 1, side view.
Histone H4 in PDB entry 5oy7, assembly 1, top view.
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Histone H2A type 1
Chains: C, G, K, O, S, W, a, e
Length: 130 amino acids
Theoretical weight: 14.11 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 1-130; Coverage: 100%)
Pfam:
InterPro:
Histone H2A type 1 in PDB entry 5oy7, assembly 1, front view.
Histone H2A type 1 in PDB entry 5oy7, assembly 1, side view.
Histone H2A type 1 in PDB entry 5oy7, assembly 1, top view.
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DNA chain g
Name: DNA (619-MER)
Representative chains: g
Length: 634 nucleotides
Theoretical weight: 194.77 KDa
DNA (619-MER) in PDB entry 5oy7, assembly 1, front view.
DNA (619-MER) in PDB entry 5oy7, assembly 1, side view.
DNA (619-MER) in PDB entry 5oy7, assembly 1, top view.
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DNA chain h
Name: DNA (619-MER)
Representative chains: h
Length: 628 nucleotides
Theoretical weight: 195.07 KDa
DNA (619-MER) in PDB entry 5oy7, assembly 1, front view.
DNA (619-MER) in PDB entry 5oy7, assembly 1, side view.
DNA (619-MER) in PDB entry 5oy7, assembly 1, top view.
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