› 8x1c

Electron Microscopy
3.2Å resolution

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

Released:
DOI: 10.2210/pdb8x1c/pdb
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
Primary publication:
Structural insights into histone exchange by human SRCAP complex.
Yu J, Sui F, Gu F, Li W, Yu Z, Wang Q, He S, Wang L, Xu Y
OpenAccess logo Cell Discov 10 15 (2024)
PMID: 38331872
Related structures: EMD-37990

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 25-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-240746 (preferred)
Entry contents:
14 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (16 distinct):
Histone H2A type 1-C Chains: A, E
Molecule details ›
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
Sequence domains:
Histone H2B type 1-C/E/F/G/I Chains: B, F
Molecule details ›
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
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H3.1 Chains: C, G
Molecule details ›
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
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: D, H
Molecule details ›
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
Sequence domains: Centromere kinetochore component CENP-T histone fold
Helicase SRCAP Chain: I
Molecule details ›
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
Sequence domains:
Vacuolar protein sorting-associated protein 72 homolog Chain: J
Molecule details ›
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
Sequence domains:
Actin-related protein 6 Chain: K
Molecule details ›
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
Sequence domains: Actin
Zinc finger HIT domain-containing protein 1 Chain: L
Molecule details ›
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
Sequence domains: HIT zinc finger
RuvB-like 1 Chains: M, O, Q
Molecule details ›
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
Sequence domains:
RuvB-like 2 Chains: N, P, R
Molecule details ›
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
Sequence domains:
Actin, cytoplasmic 1 Chains: S, U
Molecule details ›
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
Sequence domains: Actin
Actin-like protein 6A Chain: T
Molecule details ›
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
Sequence domains: Actin
DNA methyltransferase 1-associated protein 1 Chain: V
Molecule details ›
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
Sequence domains:
YEATS domain-containing protein 4 Chain: W
Molecule details ›
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
Sequence domains: YEATS family
DNA (147-MER) Chain: X
Molecule details ›
Chain: X
Length: 147 nucleotides
Theoretical weight: 45.64 KDa
DNA (147-MER) Chain: Y
Molecule details ›
Chain: Y
Length: 147 nucleotides
Theoretical weight: 45.11 KDa

Ligands and Environments

2 bound ligands:
Ligand ADP 7 x ADP
Ligand ATP 3 x ATP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-37990
Expression systems:
  • Escherichia coli
  • Homo sapiens

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