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Nucleosome containing methylated Sat2L DNA

X-ray diffraction
2.632Å resolution
PDB entry 5cpk coloured by chain, front view.
PDB entry 5cpk coloured by chain, side view.
PDB entry 5cpk coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero decamer (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, variant H3.1-H2A.2-H2B.1 and DNA
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Multimeric state: hetero decamer
Accessible surface area: 70540.08 Å2
Buried surface area: 62539.19 Å2
Dissociation area: 3,573.06 Å2
Dissociation energy (ΔGdiss): 46.39 kcal/mol
Dissociation entropy (TΔSdiss): 14.3 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-118511

Macromolecules

Histone H3.1
Chains: A, E
Length: 139 amino acids
Theoretical weight: 15.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
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
Histone H3.1 in PDB entry 5cpk, assembly 1, front view.
Histone H3.1 in PDB entry 5cpk, assembly 1, side view.
Histone H3.1 in PDB entry 5cpk, assembly 1, top view.
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Histone H4
Chains: B, F
Length: 106 amino acids
Theoretical weight: 11.68 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
Histone H4 in PDB entry 5cpk, assembly 1, front view.
Histone H4 in PDB entry 5cpk, assembly 1, side view.
Histone H4 in PDB entry 5cpk, assembly 1, top view.
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Histone H2A type 1-B/E
Chains: C, G
Length: 133 amino acids
Theoretical weight: 14.45 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04908 (Residues: 1-130; Coverage: 100%)
Gene names: H2AC4, H2AC8, H2AFA, H2AFM, HIST1H2AB, HIST1H2AE
Pfam:
InterPro:
CATH: Histone, subunit A
Histone H2A type 1-B/E in PDB entry 5cpk, assembly 1, front view.
Histone H2A type 1-B/E in PDB entry 5cpk, assembly 1, side view.
Histone H2A type 1-B/E in PDB entry 5cpk, assembly 1, top view.
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Histone H2B type 1-J
Chains: D, H
Length: 129 amino acids
Theoretical weight: 14.22 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P06899 (Residues: 1-126; Coverage: 100%)
Gene names: H2BC11, H2BFR, HIST1H2BJ
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
CATH: Histone, subunit A
Histone H2B type 1-J in PDB entry 5cpk, assembly 1, front view.
Histone H2B type 1-J in PDB entry 5cpk, assembly 1, side view.
Histone H2B type 1-J in PDB entry 5cpk, assembly 1, top view.
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DNA chain I
Name: DNA (145-MER)
Representative chains: I
Length: 145 nucleotides
Theoretical weight: 45.19 KDa
DNA (145-MER) in PDB entry 5cpk, assembly 1, front view.
DNA (145-MER) in PDB entry 5cpk, assembly 1, side view.
DNA (145-MER) in PDB entry 5cpk, assembly 1, top view.
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DNA chain J
Name: DNA (145-MER)
Representative chains: J
Length: 145 nucleotides
Theoretical weight: 44.43 KDa
DNA (145-MER) in PDB entry 5cpk, assembly 1, front view.
DNA (145-MER) in PDB entry 5cpk, assembly 1, side view.
DNA (145-MER) in PDB entry 5cpk, assembly 1, top view.
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