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Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite Sequence (NCP146b)

X-ray diffraction
2.2Å resolution
PDB entry 3utb coloured by chain, front view.
PDB entry 3utb coloured by chain, side view.
PDB entry 3utb 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: 71756.76 Å2
Buried surface area: 61134.8 Å2
Dissociation area: 4,587.13 Å2
Dissociation energy (ΔGdiss): 64.38 kcal/mol
Dissociation entropy (TΔSdiss): 14.39 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117008

Macromolecules

Histone H3.2
Chains: A, E
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:
CATH: Histone, subunit A
Histone H3.2 in PDB entry 3utb, assembly 1, front view.
Histone H3.2 in PDB entry 3utb, assembly 1, side view.
Histone H3.2 in PDB entry 3utb, assembly 1, top view.
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Histone H4
Chains: B, F
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:
CATH: Histone, subunit A
Histone H4 in PDB entry 3utb, assembly 1, front view.
Histone H4 in PDB entry 3utb, assembly 1, side view.
Histone H4 in PDB entry 3utb, assembly 1, top view.
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Histone H2A type 1
Chains: C, G
Length: 129 amino acids
Theoretical weight: 13.98 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 2-130; Coverage: 99%)
Pfam:
InterPro:
CATH: Histone, subunit A
Histone H2A type 1 in PDB entry 3utb, assembly 1, front view.
Histone H2A type 1 in PDB entry 3utb, assembly 1, side view.
Histone H2A type 1 in PDB entry 3utb, assembly 1, top view.
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Histone H2B 1.1
Chains: D, H
Length: 125 amino acids
Theoretical weight: 13.85 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 2-126; Coverage: 99%)
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
CATH: Histone, subunit A
Histone H2B 1.1 in PDB entry 3utb, assembly 1, front view.
Histone H2B 1.1 in PDB entry 3utb, assembly 1, side view.
Histone H2B 1.1 in PDB entry 3utb, assembly 1, top view.
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DNA chains I, J
Name: 146-mer DNA
Representative chains: I, J
Length: 146 nucleotides
Theoretical weight: 45.05 KDa
146-mer DNA in PDB entry 3utb, assembly 1, front view.
146-mer DNA in PDB entry 3utb, assembly 1, side view.
146-mer DNA in PDB entry 3utb, assembly 1, top view.
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