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Structural characterization of H3K56Q nucleosomes and nucleosomal arrays

X-ray diffraction
3.5Å resolution
PDB entry 3kwq coloured by chain, front view.
PDB entry 3kwq coloured by chain, side view.
PDB entry 3kwq coloured by chain, top view.
Source organism: Xenopus laevis
Assembly composition:
hetero decamer (preferred)
Entry contents: 4 distinct polypeptide molecules
1 distinct DNA molecule

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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 decamer
Accessible surface area: 73236.55 Å2
Buried surface area: 55870.53 Å2
Dissociation area: 4,508.35 Å2
Dissociation energy (ΔGdiss): 61.21 kcal/mol
Dissociation entropy (TΔSdiss): 14.38 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-116508

Macromolecules

Histone H3.2
Chains: A, E
Length: 98 amino acids
Theoretical weight: 11.5 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 39-136; Coverage: 72%)
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
CATH: Histone, subunit A
Histone H3.2 in PDB entry 3kwq, assembly 1, front view.
Histone H3.2 in PDB entry 3kwq, assembly 1, side view.
Histone H3.2 in PDB entry 3kwq, assembly 1, top view.
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Histone H4
Chains: B, F
Length: 83 amino acids
Theoretical weight: 9.41 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 21-103; Coverage: 81%)
Pfam: Centromere kinetochore component CENP-T histone fold
InterPro:
CATH: Histone, subunit A
Histone H4 in PDB entry 3kwq, assembly 1, front view.
Histone H4 in PDB entry 3kwq, assembly 1, side view.
Histone H4 in PDB entry 3kwq, assembly 1, top view.
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Histone H2A type 1
Chains: C, G
Length: 107 amino acids
Theoretical weight: 11.72 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 15-121; Coverage: 82%)
Pfam:
InterPro:
CATH: Histone, subunit A
Histone H2A type 1 in PDB entry 3kwq, assembly 1, front view.
Histone H2A type 1 in PDB entry 3kwq, assembly 1, side view.
Histone H2A type 1 in PDB entry 3kwq, assembly 1, top view.
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Histone H2B 1.1
Chains: D, H
Length: 93 amino acids
Theoretical weight: 10.38 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 34-126; Coverage: 74%)
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
CATH: Histone, subunit A
Histone H2B 1.1 in PDB entry 3kwq, assembly 1, front view.
Histone H2B 1.1 in PDB entry 3kwq, assembly 1, side view.
Histone H2B 1.1 in PDB entry 3kwq, assembly 1, top view.
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DNA chains I, J
Name: DNA (146-MER)
Representative chains: I, J
Length: 146 nucleotides
Theoretical weight: 45.05 KDa
DNA (146-MER) in PDB entry 3kwq, assembly 1, front view.
DNA (146-MER) in PDB entry 3kwq, assembly 1, side view.
DNA (146-MER) in PDB entry 3kwq, assembly 1, top view.
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