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Structure of a nucleosome composed of a palindromic 167-base pair blunt-ended DNA fragment

X-ray diffraction
3.261Å resolution
PDB entry 8qkt coloured by chain, front view.
PDB entry 8qkt coloured by chain, side view.
PDB entry 8qkt coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero decamer (preferred)
Entry contents: 6 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1
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Multimeric state: hetero decamer
Accessible surface area: 79587.91 Å2
Buried surface area: 61036.18 Å2
Dissociation area: 7,336.24 Å2
Dissociation energy (ΔGdiss): 101.45 kcal/mol
Dissociation entropy (TΔSdiss): 28.79 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-232331
Assembly 2 (preferred)
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Multimeric state: hetero decamer
Accessible surface area: 79718.53 Å2
Buried surface area: 60332.33 Å2
Dissociation area: 7,339.28 Å2
Dissociation energy (ΔGdiss): 98.75 kcal/mol
Dissociation entropy (TΔSdiss): 28.79 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-232331

Macromolecules

Histone H3.1
Chains: AAA, EEE, KKK, OOO
Length: 98 amino acids
Theoretical weight: 11.5 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P68431 (Residues: 39-136; Coverage: 72%)
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
Histone H3.1 in PDB entry 8qkt, assembly 2, front view.
Histone H3.1 in PDB entry 8qkt, assembly 2, side view.
Histone H3.1 in PDB entry 8qkt, assembly 2, top view.
PDBe-KB: UniProt Coverage View: P68431  
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Histone H4
Chains: BBB, FFF, LLL, PPP
Length: 79 amino acids
Theoretical weight: 8.91 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A8C1JQV0 (Residues: 14-92; Coverage: 86%)
Pfam: Centromere kinetochore component CENP-T histone fold
Histone H4 in PDB entry 8qkt, assembly 2, front view.
Histone H4 in PDB entry 8qkt, assembly 2, side view.
Histone H4 in PDB entry 8qkt, assembly 2, top view.
PDBe-KB: UniProt Coverage View: A0A8C1JQV0  
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Histone H2A
Chains: CCC, MMM
Length: 105 amino acids
Theoretical weight: 11.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: H2QSF5 (Residues: 15-119; Coverage: 81%)
Gene names: H2AC4, H2AC8
Pfam:
Histone H2A in PDB entry 8qkt, assembly 2, front view.
Histone H2A in PDB entry 8qkt, assembly 2, side view.
Histone H2A in PDB entry 8qkt, assembly 2, top view.
PDBe-KB: UniProt Coverage View: H2QSF5  
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Histone H2B type 1-J
Chains: DDD, NNN
Length: 96 amino acids
Theoretical weight: 10.78 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P06899 (Residues: 30-125; Coverage: 76%)
Gene names: H2BC11, H2BFR, HIST1H2BJ
Pfam: Core histone H2A/H2B/H3/H4
Histone H2B type 1-J in PDB entry 8qkt, assembly 2, front view.
Histone H2B type 1-J in PDB entry 8qkt, assembly 2, side view.
Histone H2B type 1-J in PDB entry 8qkt, assembly 2, top view.
PDBe-KB: UniProt Coverage View: P06899  
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Histone H2A
Chains: GGG, QQQ
Length: 103 amino acids
Theoretical weight: 11.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A2Y9FT95 (Residues: 17-119; Coverage: 79%)
Gene names: LOC102977259, LOC102978667
Pfam:
Histone H2A in PDB entry 8qkt, assembly 2, front view.
Histone H2A in PDB entry 8qkt, assembly 2, side view.
Histone H2A in PDB entry 8qkt, assembly 2, top view.
PDBe-KB: UniProt Coverage View: A0A2Y9FT95  
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Histone H2B type 1-J
Chains: HHH, RRR
Length: 97 amino acids
Theoretical weight: 10.91 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P06899 (Residues: 30-126; Coverage: 77%)
Gene names: H2BC11, H2BFR, HIST1H2BJ
Pfam: Core histone H2A/H2B/H3/H4
Histone H2B type 1-J in PDB entry 8qkt, assembly 2, front view.
Histone H2B type 1-J in PDB entry 8qkt, assembly 2, side view.
Histone H2B type 1-J in PDB entry 8qkt, assembly 2, top view.
PDBe-KB: UniProt Coverage View: P06899  
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DNA chains III, SSS
Name: DNA (167-MER)
Representative chains: III, SSS
Length: 167 nucleotides
Theoretical weight: 51.55 KDa
DNA (167-MER) in PDB entry 8qkt, assembly 2, front view.
DNA (167-MER) in PDB entry 8qkt, assembly 2, side view.
DNA (167-MER) in PDB entry 8qkt, assembly 2, top view.
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DNA chains JJJ, TTT
Name: DNA (167-MER)
Representative chains: JJJ, TTT
Length: 167 nucleotides
Theoretical weight: 51.54 KDa
DNA (167-MER) in PDB entry 8qkt, assembly 2, front view.
DNA (167-MER) in PDB entry 8qkt, assembly 2, side view.
DNA (167-MER) in PDB entry 8qkt, assembly 2, top view.
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