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Class2C : CENP-A nucleosome in complex with CENP-C central region

Electron Microscopy
3.7Å resolution
PDB entry 6sef coloured by chain, front view.
PDB entry 6sef coloured by chain, side view.
PDB entry 6sef coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero undecamer (preferred)
Entry contents: 5 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero undecamer
Accessible surface area: 75802.18 Å2
Buried surface area: 54287.06 Å2
Dissociation area: 852.73 Å2
Dissociation energy (ΔGdiss): -3.93 kcal/mol
Dissociation entropy (TΔSdiss): 9.17 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-120608

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 6sef, assembly 1, front view.
Histone H3-like centromeric protein A in PDB entry 6sef, assembly 1, side view.
Histone H3-like centromeric protein A in PDB entry 6sef, 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 6sef, assembly 1, front view.
Histone H4 in PDB entry 6sef, assembly 1, side view.
Histone H4 in PDB entry 6sef, assembly 1, top view.
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Histone H2A type 2-A
Chains: C, 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 6sef, assembly 1, front view.
Histone H2A type 2-A in PDB entry 6sef, assembly 1, side view.
Histone H2A type 2-A in PDB entry 6sef, 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 6sef, assembly 1, front view.
Histone H2B type 1-C/E/F/G/I in PDB entry 6sef, assembly 1, side view.
Histone H2B type 1-C/E/F/G/I in PDB entry 6sef, assembly 1, top view.
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Centromere protein C
Chain: V
Length: 124 amino acids
Theoretical weight: 14.2 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q03188 (Residues: 426-537; Coverage: 12%)
Gene names: CENPC, CENPC1, ICEN7
Pfam: Centromere assembly component CENP-C middle DNMT3B-binding region
InterPro: CENP-C, middle DNMT3B-binding domain
Centromere protein C in PDB entry 6sef, assembly 1, front view.
Centromere protein C in PDB entry 6sef, assembly 1, side view.
Centromere protein C in PDB entry 6sef, 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 6sef, assembly 1, front view.
DNA (145-MER) in PDB entry 6sef, assembly 1, side view.
DNA (145-MER) in PDB entry 6sef, 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 6sef, assembly 1, front view.
DNA (145-MER) in PDB entry 6sef, assembly 1, side view.
DNA (145-MER) in PDB entry 6sef, assembly 1, top view.
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