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Cryo-EM structure of BAP1-ASXL1 bound to chromatosome

Electron Microscopy
3Å resolution
PDB entry 8h1t coloured by chain, front view.
PDB entry 8h1t coloured by chain, side view.
PDB entry 8h1t coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero tetradecamer (preferred)
Entry contents: 8 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero tetradecamer
Accessible surface area: 106377.04 Å2
Buried surface area: 71919.15 Å2
Dissociation area: 807.83 Å2
Dissociation energy (ΔGdiss): 2.01 kcal/mol
Dissociation entropy (TΔSdiss): 11.34 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-122602

Macromolecules

Histone H3.1
Chains: A, E
Length: 136 amino acids
Theoretical weight: 15.44 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
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:
Histone H3.1 in PDB entry 8h1t, assembly 1, front view.
Histone H3.1 in PDB entry 8h1t, assembly 1, side view.
Histone H3.1 in PDB entry 8h1t, 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 8h1t, assembly 1, front view.
Histone H4 in PDB entry 8h1t, assembly 1, side view.
Histone H4 in PDB entry 8h1t, assembly 1, top view.
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Histone H2A type 1-D
Chains: C, G
Length: 130 amino acids
Theoretical weight: 14.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P20671 (Residues: 1-130; Coverage: 100%)
Gene names: H2AC7, H2AFG, HIST1H2AD
Pfam:
InterPro:
Histone H2A type 1-D in PDB entry 8h1t, assembly 1, front view.
Histone H2A type 1-D in PDB entry 8h1t, assembly 1, side view.
Histone H2A type 1-D in PDB entry 8h1t, assembly 1, top view.
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Histone H2B type 2-E
Chains: D, H
Length: 126 amino acids
Theoretical weight: 13.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q16778 (Residues: 1-126; Coverage: 100%)
Gene names: H2BC21, H2BFQ, HIST2H2BE
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
Histone H2B type 2-E in PDB entry 8h1t, assembly 1, front view.
Histone H2B type 2-E in PDB entry 8h1t, assembly 1, side view.
Histone H2B type 2-E in PDB entry 8h1t, assembly 1, top view.
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Histone H1.4
Chain: K
Length: 229 amino acids
Theoretical weight: 23.19 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P10412 (Residues: 1-219; Coverage: 100%)
Gene names: H1-4, H1F4, HIST1H1E
Pfam: linker histone H1 and H5 family
InterPro:
Histone H1.4 in PDB entry 8h1t, assembly 1, front view.
Histone H1.4 in PDB entry 8h1t, assembly 1, side view.
Histone H1.4 in PDB entry 8h1t, assembly 1, top view.
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Ubiquitin carboxyl-terminal hydrolase BAP1
Chain: L
Length: 729 amino acids
Theoretical weight: 80.46 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q92560 (Residues: 1-729; Coverage: 100%)
Gene names: BAP1, KIAA0272, hucep-6
Pfam:
InterPro:
Ubiquitin carboxyl-terminal hydrolase BAP1 in PDB entry 8h1t, assembly 1, front view.
Ubiquitin carboxyl-terminal hydrolase BAP1 in PDB entry 8h1t, assembly 1, side view.
Ubiquitin carboxyl-terminal hydrolase BAP1 in PDB entry 8h1t, assembly 1, top view.
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Ubiquitin
Chain: M
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Pfam: Ubiquitin family
InterPro:
Ubiquitin in PDB entry 8h1t, assembly 1, front view.
Ubiquitin in PDB entry 8h1t, assembly 1, side view.
Ubiquitin in PDB entry 8h1t, assembly 1, top view.
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Polycomb group protein ASXL1
Chain: N
Length: 378 amino acids
Theoretical weight: 41.79 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8IXJ9 (Residues: 1-378; Coverage: 25%)
Gene names: ASXL1, KIAA0978
Pfam:
InterPro:
Polycomb group protein ASXL1 in PDB entry 8h1t, assembly 1, front view.
Polycomb group protein ASXL1 in PDB entry 8h1t, assembly 1, side view.
Polycomb group protein ASXL1 in PDB entry 8h1t, assembly 1, top view.
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DNA chain I
Name: DNA (187-MER)
Representative chains: I
Length: 187 nucleotides
Theoretical weight: 57.44 KDa
DNA (187-MER) in PDB entry 8h1t, assembly 1, front view.
DNA (187-MER) in PDB entry 8h1t, assembly 1, side view.
DNA (187-MER) in PDB entry 8h1t, assembly 1, top view.
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DNA chain J
Name: DNA (187-MER)
Representative chains: J
Length: 187 nucleotides
Theoretical weight: 58.03 KDa
DNA (187-MER) in PDB entry 8h1t, assembly 1, front view.
DNA (187-MER) in PDB entry 8h1t, assembly 1, side view.
DNA (187-MER) in PDB entry 8h1t, assembly 1, top view.
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