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Crystal structure of the nucleosome core particle containing the histone domain of macroH2A

X-ray diffraction
3Å resolution
PDB entry 1u35 coloured by chain, front view.
PDB entry 1u35 coloured by chain, side view.
PDB entry 1u35 coloured by chain, top view.
Source organisms:
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: 71677.98 Å2
Buried surface area: 56332.17 Å2
Dissociation area: 7,271.84 Å2
Dissociation energy (ΔGdiss): 90.92 kcal/mol
Dissociation entropy (TΔSdiss): 28.7 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-114677

Macromolecules

Histone H3.1
Chains: A, E
Length: 136 amino acids
Theoretical weight: 15.44 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P68433 (Residues: 1-136; Coverage: 100%)
Gene names: H3.1-221, H3.1-291, H3.1-I, H3a, H3c1, H3c10, H3c11, H3c8, H3g, H3h, H3i, Hist1h3a, Hist1h3g, Hist1h3h, Hist1h3i
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
CATH: Histone, subunit A
SCOP: Nucleosome core histones
Histone H3.1 in PDB entry 1u35, assembly 1, front view.
Histone H3.1 in PDB entry 1u35, assembly 1, side view.
Histone H3.1 in PDB entry 1u35, assembly 1, top view.
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Histone H4
Chains: B, F
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P62806 (Residues: 1-103; Coverage: 100%)
Gene names: H4-12, H4-53, H4c1, H4c11, H4c12, H4c14, H4c16, H4c2, H4c3, H4c4, H4c6, H4c8, H4c9, H4f16, Hist1h4a, Hist1h4b, Hist1h4c, Hist1h4d, Hist1h4f, Hist1h4h, Hist1h4i, Hist1h4j, Hist1h4k, Hist1h4m, Hist2h4, Hist2h4a, Hist4h4
Pfam: Centromere kinetochore component CENP-T histone fold
InterPro:
CATH: Histone, subunit A
SCOP: Nucleosome core histones
Histone H4 in PDB entry 1u35, assembly 1, front view.
Histone H4 in PDB entry 1u35, assembly 1, side view.
Histone H4 in PDB entry 1u35, assembly 1, top view.
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Core histone macro-H2A.1
Chains: C, G
Length: 120 amino acids
Theoretical weight: 12.98 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O75367 (Residues: 1-120; Coverage: 33%)
Gene names: H2AFY, MACROH2A1
Pfam:
InterPro:
CATH: Histone, subunit A
SCOP: Nucleosome core histones
Core histone macro-H2A.1 in PDB entry 1u35, assembly 1, front view.
Core histone macro-H2A.1 in PDB entry 1u35, assembly 1, side view.
Core histone macro-H2A.1 in PDB entry 1u35, assembly 1, top view.
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H2B.U histone 2
Chains: D, H
Length: 126 amino acids
Theoretical weight: 14.03 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9D2U9 (Residues: 1-126; Coverage: 100%)
Gene names: H2bu2, Hist3h2ba
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
CATH: Histone, subunit A
SCOP: Nucleosome core histones
H2B.U histone 2 in PDB entry 1u35, assembly 1, front view.
H2B.U histone 2 in PDB entry 1u35, assembly 1, side view.
H2B.U histone 2 in PDB entry 1u35, assembly 1, top view.
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DNA chains I, J
Name: alpha-satellite DNA
Representative chains: I, J
Length: 146 nucleotides
Theoretical weight: 45.05 KDa
alpha-satellite DNA in PDB entry 1u35, assembly 1, front view.
alpha-satellite DNA in PDB entry 1u35, assembly 1, side view.
alpha-satellite DNA in PDB entry 1u35, assembly 1, top view.
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