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Crystal structure of human nucleosome core particle

X-ray diffraction
2.5Å resolution
PDB entry 2cv5 coloured by chain, front view.
PDB entry 2cv5 coloured by chain, side view.
PDB entry 2cv5 coloured by chain, top view.
Source organism: Homo sapiens
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: 71424.67 Å2
Buried surface area: 58793.25 Å2
Dissociation area: 4,427.83 Å2
Dissociation energy (ΔGdiss): 78.37 kcal/mol
Dissociation entropy (TΔSdiss): 14.29 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-115152

Macromolecules

Histone H3.1
Chains: A, E
Length: 136 amino acids
Theoretical weight: 15.44 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P68431 (Residues: 1-136; Coverage: 100%)
Gene names: H3C1, H3C10, H3C11, H3C12, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3FA, H3FB, H3FC HIST1H3C, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
CATH: Histone, subunit A
SCOP: Nucleosome core histones
Histone H3.1 in PDB entry 2cv5, assembly 1, front view.
Histone H3.1 in PDB entry 2cv5, assembly 1, side view.
Histone H3.1 in PDB entry 2cv5, assembly 1, top view.
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Histone H4
Chains: B, F
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62805 (Residues: 1-103; Coverage: 100%)
Gene names: H4-16, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4C1, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4
Pfam: Centromere kinetochore component CENP-T histone fold
InterPro:
CATH: Histone, subunit A
SCOP: Nucleosome core histones
Histone H4 in PDB entry 2cv5, assembly 1, front view.
Histone H4 in PDB entry 2cv5, assembly 1, side view.
Histone H4 in PDB entry 2cv5, assembly 1, top view.
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Histone H2A type 1-B/E
Chains: C, G
Length: 130 amino acids
Theoretical weight: 14.17 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P04908 (Residues: 1-130; Coverage: 100%)
Gene names: H2AC4, H2AC8, H2AFA, H2AFM, HIST1H2AB, HIST1H2AE
Pfam:
InterPro:
CATH: Histone, subunit A
SCOP: Nucleosome core histones
Histone H2A type 1-B/E in PDB entry 2cv5, assembly 1, front view.
Histone H2A type 1-B/E in PDB entry 2cv5, assembly 1, side view.
Histone H2A type 1-B/E in PDB entry 2cv5, assembly 1, top view.
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Histone H2B type 1-K
Chains: D, H
Length: 126 amino acids
Theoretical weight: 13.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60814 (Residues: 1-126; Coverage: 100%)
Gene names: H2BC12, H2BFT, HIRIP1, HIST1H2BK
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
CATH: Histone, subunit A
SCOP: Nucleosome core histones
Histone H2B type 1-K in PDB entry 2cv5, assembly 1, front view.
Histone H2B type 1-K in PDB entry 2cv5, assembly 1, side view.
Histone H2B type 1-K in PDB entry 2cv5, 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 2cv5, assembly 1, front view.
DNA (146-MER) in PDB entry 2cv5, assembly 1, side view.
DNA (146-MER) in PDB entry 2cv5, assembly 1, top view.
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