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Class 1 : CENP-A nucleosome

Electron Microscopy
3.8Å resolution
PDB entry 6se0 coloured by chain, front view.
PDB entry 6se0 coloured by chain, side view.
PDB entry 6se0 coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero decamer (preferred)
Entry contents: 5 distinct polypeptide molecules
2 distinct DNA molecules

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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: 75037.9 Å2
Buried surface area: 56874.51 Å2
Dissociation area: 5,869.36 Å2
Dissociation energy (ΔGdiss): 76.55 kcal/mol
Dissociation entropy (TΔSdiss): 16.13 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-120605

Macromolecules

Histone H3-like centromeric protein A
Chains: A, E
Length: 140 amino acids
Theoretical weight: 16.02 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P49450 (Residues: 1-140; Coverage: 100%)
Gene name: CENPA
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
Histone H3-like centromeric protein A in PDB entry 6se0, assembly 1, front view.
Histone H3-like centromeric protein A in PDB entry 6se0, assembly 1, side view.
Histone H3-like centromeric protein A in PDB entry 6se0, 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:
Histone H4 in PDB entry 6se0, assembly 1, front view.
Histone H4 in PDB entry 6se0, assembly 1, side view.
Histone H4 in PDB entry 6se0, assembly 1, top view.
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Histone H2A type 2-A
Chain: C
Length: 129 amino acids
Theoretical weight: 13.99 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6FI13 (Residues: 2-130; Coverage: 99%)
Gene names: H2AC18, H2AC19, H2AFO, HIST2H2AA, HIST2H2AA3, HIST2H2AA4
Pfam:
InterPro:
Histone H2A type 2-A in PDB entry 6se0, assembly 1, front view.
Histone H2A type 2-A in PDB entry 6se0, assembly 1, side view.
Histone H2A type 2-A in PDB entry 6se0, assembly 1, top view.
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Histone H2B type 1-C/E/F/G/I
Chains: D, H
Length: 126 amino acids
Theoretical weight: 13.94 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62807 (Residues: 1-126; Coverage: 100%)
Gene names: H2BC10, H2BC4, H2BC6, H2BC7, H2BC8, H2BFA, H2BFG, H2BFH, H2BFK, H2BFL, HIST1H2BC, HIST1H2BE, HIST1H2BF, HIST1H2BG, HIST1H2BI
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
Histone H2B type 1-C/E/F/G/I in PDB entry 6se0, assembly 1, front view.
Histone H2B type 1-C/E/F/G/I in PDB entry 6se0, assembly 1, side view.
Histone H2B type 1-C/E/F/G/I in PDB entry 6se0, assembly 1, top view.
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Histone H2A type 2-A
Chain: G
Length: 130 amino acids
Theoretical weight: 14.13 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6FI13 (Residues: 1-130; Coverage: 100%)
Gene names: H2AC18, H2AC19, H2AFO, HIST2H2AA, HIST2H2AA3, HIST2H2AA4
Pfam:
InterPro:
Histone H2A type 2-A in PDB entry 6se0, assembly 1, front view.
Histone H2A type 2-A in PDB entry 6se0, assembly 1, side view.
Histone H2A type 2-A in PDB entry 6se0, assembly 1, top view.
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DNA chain I
Name: DNA (145-MER)
Representative chains: I
Length: 145 nucleotides
Theoretical weight: 44.52 KDa
DNA (145-MER) in PDB entry 6se0, assembly 1, front view.
DNA (145-MER) in PDB entry 6se0, assembly 1, side view.
DNA (145-MER) in PDB entry 6se0, assembly 1, top view.
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DNA chain J
Name: DNA (145-MER)
Representative chains: J
Length: 145 nucleotides
Theoretical weight: 44.99 KDa
DNA (145-MER) in PDB entry 6se0, assembly 1, front view.
DNA (145-MER) in PDB entry 6se0, assembly 1, side view.
DNA (145-MER) in PDB entry 6se0, assembly 1, top view.
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