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Structure of nucleosome-bound SRCAP-C in the ADP-bound state

Electron Microscopy
3.2Å resolution
PDB entry 8x1c coloured by chain, front view.
PDB entry 8x1c coloured by chain, side view.
PDB entry 8x1c coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero 25-mer (preferred)
Entry contents: 14 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 25-mer
Accessible surface area: 296090.35 Å2
Buried surface area: 162889.74 Å2
Dissociation area: 885.46 Å2
Dissociation energy (ΔGdiss): 0.08 kcal/mol
Dissociation entropy (TΔSdiss): 14.12 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-240746

Macromolecules

Histone H2A type 1-C
Chains: A, E
Length: 130 amino acids
Theoretical weight: 14.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q93077 (Residues: 1-130; Coverage: 100%)
Gene names: H2AC6, H2AFL, HIST1H2AC
Pfam:
Histone H2A type 1-C in PDB entry 8x1c, assembly 1, front view.
Histone H2A type 1-C in PDB entry 8x1c, assembly 1, side view.
Histone H2A type 1-C in PDB entry 8x1c, assembly 1, top view.
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Histone H2B type 1-C/E/F/G/I
Chains: B, F
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
Histone H2B type 1-C/E/F/G/I in PDB entry 8x1c, assembly 1, front view.
Histone H2B type 1-C/E/F/G/I in PDB entry 8x1c, assembly 1, side view.
Histone H2B type 1-C/E/F/G/I in PDB entry 8x1c, assembly 1, top view.
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Histone H3.1
Chains: C, G
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
Histone H3.1 in PDB entry 8x1c, assembly 1, front view.
Histone H3.1 in PDB entry 8x1c, assembly 1, side view.
Histone H3.1 in PDB entry 8x1c, assembly 1, top view.
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Histone H4
Chains: D, H
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
Histone H4 in PDB entry 8x1c, assembly 1, front view.
Histone H4 in PDB entry 8x1c, assembly 1, side view.
Histone H4 in PDB entry 8x1c, assembly 1, top view.
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Helicase SRCAP
Chain: I
Length: 3230 amino acids
Theoretical weight: 343.92 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q6ZRS2 (Residues: 1-3230; Coverage: 100%)
Gene names: KIAA0309, SRCAP
Pfam:
Helicase SRCAP in PDB entry 8x1c, assembly 1, front view.
Helicase SRCAP in PDB entry 8x1c, assembly 1, side view.
Helicase SRCAP in PDB entry 8x1c, assembly 1, top view.
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Vacuolar protein sorting-associated protein 72 homolog
Chain: J
Length: 364 amino acids
Theoretical weight: 40.66 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q15906 (Residues: 1-364; Coverage: 100%)
Gene names: TCFL1, VPS72, YL1
Pfam:
Vacuolar protein sorting-associated protein 72 homolog in PDB entry 8x1c, assembly 1, front view.
Vacuolar protein sorting-associated protein 72 homolog in PDB entry 8x1c, assembly 1, side view.
Vacuolar protein sorting-associated protein 72 homolog in PDB entry 8x1c, assembly 1, top view.
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Actin-related protein 6
Chain: K
Length: 396 amino acids
Theoretical weight: 45.86 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9GZN1 (Residues: 1-396; Coverage: 100%)
Gene names: ACTR6, CDA12
Pfam: Actin
Actin-related protein 6 in PDB entry 8x1c, assembly 1, front view.
Actin-related protein 6 in PDB entry 8x1c, assembly 1, side view.
Actin-related protein 6 in PDB entry 8x1c, assembly 1, top view.
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Zinc finger HIT domain-containing protein 1
Chain: L
Length: 154 amino acids
Theoretical weight: 17.57 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O43257 (Residues: 1-154; Coverage: 100%)
Gene names: CGBP1, ZNFN4A1, ZNHIT1
Pfam: HIT zinc finger
Zinc finger HIT domain-containing protein 1 in PDB entry 8x1c, assembly 1, front view.
Zinc finger HIT domain-containing protein 1 in PDB entry 8x1c, assembly 1, side view.
Zinc finger HIT domain-containing protein 1 in PDB entry 8x1c, assembly 1, top view.
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RuvB-like 1
Chains: M, O, Q
Length: 456 amino acids
Theoretical weight: 50.3 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9Y265 (Residues: 1-456; Coverage: 100%)
Gene names: INO80H, NMP238, RUVBL1, TIP49, TIP49A
Pfam:
RuvB-like 1 in PDB entry 8x1c, assembly 1, front view.
RuvB-like 1 in PDB entry 8x1c, assembly 1, side view.
RuvB-like 1 in PDB entry 8x1c, assembly 1, top view.
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RuvB-like 2
Chains: N, P, R
Length: 463 amino acids
Theoretical weight: 51.22 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9Y230 (Residues: 1-463; Coverage: 100%)
Gene names: CGI-46, INO80J, RUVBL2, TIP48, TIP49B
Pfam:
RuvB-like 2 in PDB entry 8x1c, assembly 1, front view.
RuvB-like 2 in PDB entry 8x1c, assembly 1, side view.
RuvB-like 2 in PDB entry 8x1c, assembly 1, top view.
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Actin, cytoplasmic 1
Chains: S, U
Length: 375 amino acids
Theoretical weight: 41.78 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P60709 (Residues: 1-375; Coverage: 100%)
Gene name: ACTB
Pfam: Actin
Actin, cytoplasmic 1 in PDB entry 8x1c, assembly 1, front view.
Actin, cytoplasmic 1 in PDB entry 8x1c, assembly 1, side view.
Actin, cytoplasmic 1 in PDB entry 8x1c, assembly 1, top view.
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Actin-like protein 6A
Chain: T
Length: 429 amino acids
Theoretical weight: 47.51 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O96019 (Residues: 1-429; Coverage: 100%)
Gene names: ACTL6A, BAF53, BAF53A, INO80K
Pfam: Actin
Actin-like protein 6A in PDB entry 8x1c, assembly 1, front view.
Actin-like protein 6A in PDB entry 8x1c, assembly 1, side view.
Actin-like protein 6A in PDB entry 8x1c, assembly 1, top view.
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DNA methyltransferase 1-associated protein 1
Chain: V
Length: 467 amino acids
Theoretical weight: 53.09 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9NPF5 (Residues: 1-467; Coverage: 100%)
Gene names: DMAP1, KIAA1425
Pfam:
DNA methyltransferase 1-associated protein 1 in PDB entry 8x1c, assembly 1, front view.
DNA methyltransferase 1-associated protein 1 in PDB entry 8x1c, assembly 1, side view.
DNA methyltransferase 1-associated protein 1 in PDB entry 8x1c, assembly 1, top view.
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YEATS domain-containing protein 4
Chain: W
Length: 227 amino acids
Theoretical weight: 26.54 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O95619 (Residues: 1-227; Coverage: 100%)
Gene names: GAS41, YEATS4
Pfam: YEATS family
YEATS domain-containing protein 4 in PDB entry 8x1c, assembly 1, front view.
YEATS domain-containing protein 4 in PDB entry 8x1c, assembly 1, side view.
YEATS domain-containing protein 4 in PDB entry 8x1c, assembly 1, top view.
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DNA chain X
Name: DNA (147-MER)
Representative chains: X
Length: 147 nucleotides
Theoretical weight: 45.64 KDa
DNA (147-MER) in PDB entry 8x1c, assembly 1, front view.
DNA (147-MER) in PDB entry 8x1c, assembly 1, side view.
DNA (147-MER) in PDB entry 8x1c, assembly 1, top view.
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DNA chain Y
Name: DNA (147-MER)
Representative chains: Y
Length: 147 nucleotides
Theoretical weight: 45.11 KDa
DNA (147-MER) in PDB entry 8x1c, assembly 1, front view.
DNA (147-MER) in PDB entry 8x1c, assembly 1, side view.
DNA (147-MER) in PDB entry 8x1c, assembly 1, top view.
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