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X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution

X-ray diffraction
2Å resolution
PDB entry 1kx3 coloured by chain, front view.
PDB entry 1kx3 coloured by chain, side view.
PDB entry 1kx3 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: 72891.56 Å2
Buried surface area: 58164.83 Å2
Dissociation area: 4,518.48 Å2
Dissociation energy (ΔGdiss): 73.69 kcal/mol
Dissociation entropy (TΔSdiss): 14.46 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-114098

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
SCOP: Nucleosome core histones
Histone H3.2 in PDB entry 1kx3, assembly 1, front view.
Histone H3.2 in PDB entry 1kx3, assembly 1, side view.
Histone H3.2 in PDB entry 1kx3, 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
SCOP: Nucleosome core histones
Histone H4 in PDB entry 1kx3, assembly 1, front view.
Histone H4 in PDB entry 1kx3, assembly 1, side view.
Histone H4 in PDB entry 1kx3, assembly 1, top view.
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Histone H2A type 1
Chains: C, G
Length: 128 amino acids
Theoretical weight: 13.91 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 2-130; Coverage: 99%)
Pfam:
InterPro:
CATH: Histone, subunit A
SCOP: Nucleosome core histones
Histone H2A type 1 in PDB entry 1kx3, assembly 1, front view.
Histone H2A type 1 in PDB entry 1kx3, assembly 1, side view.
Histone H2A type 1 in PDB entry 1kx3, 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
SCOP: Nucleosome core histones
Histone H2B 1.1 in PDB entry 1kx3, assembly 1, front view.
Histone H2B 1.1 in PDB entry 1kx3, assembly 1, side view.
Histone H2B 1.1 in PDB entry 1kx3, assembly 1, top view.
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DNA chains I, J
Name: DNA (5'(ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT)3')
Representative chains: I, J
Length: 146 nucleotides
Theoretical weight: 45.05 KDa
DNA (5'(ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT)3') in PDB entry 1kx3, assembly 1, front view.
DNA (5'(ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT)3') in PDB entry 1kx3, assembly 1, side view.
DNA (5'(ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT)3') in PDB entry 1kx3, assembly 1, top view.
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