› 7y8r

Electron Microscopy
4.4Å resolution

The nucleosome-bound human PBAF complex

Released:
DOI: 10.2210/pdb7y8r/pdb
PDB entry 7y8r coloured by chain, front view.
PDB entry 7y8r coloured by chain, side view.
PDB entry 7y8r coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of nucleosome-bound human PBAF complex.
Wang L, Yu J, Yu Z, Wang Q, Li W, Ren Y, Chen Z, He S, Xu Y
Nat Commun 13 7644 (2022)
PMID: 36496390
Related structures: EMD-33684

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 27-mer (preferred)
PDBe Complex ID:
PDB-CPX-221104 (preferred)
Entry contents:
20 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (22 distinct):
Histone H3.1 Chains: A, E
Molecule details ›
Chains: A, E
Length: 135 amino acids
Theoretical weight: 15.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P68431 (Residues: 2-136; Coverage: 99%)
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: B, F
Molecule details ›
Chains: B, F
Length: 102 amino acids
Theoretical weight: 11.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P62805 (Residues: 2-103; Coverage: 99%)
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
Histone H2A type 1-C Chains: C, G
Molecule details ›
Chains: C, G
Length: 129 amino acids
Theoretical weight: 14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: Q93077 (Residues: 2-130; Coverage: 99%)
Gene names: H2AC6, H2AFL, HIST1H2AC
Sequence domains:
Histone H2B type 1-C/E/F/G/I Chains: D, H
Molecule details ›
Chains: D, H
Length: 125 amino acids
Theoretical weight: 13.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P62807 (Residues: 2-126; Coverage: 99%)
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
Unknown Chain: Z
Molecule details ›
Chain: Z
Length: 29 amino acids
Theoretical weight: 2.49 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Transcription activator BRG1 Chain: I
Molecule details ›
Chain: I
Length: 1647 amino acids
Theoretical weight: 184.92 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P51532 (Residues: 1-1647; Coverage: 100%)
Gene names: BAF190A, BRG1, SMARCA4, SNF2B, SNF2L4
Sequence domains:
Actin, cytoplasmic 1 Chain: J
Molecule details ›
Chain: J
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: K
Molecule details ›
Chain: K
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
AT-rich interactive domain-containing protein 2 Chain: L
Molecule details ›
Chain: L
Length: 1835 amino acids
Theoretical weight: 197.58 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q68CP9 (Residues: 1-1835; Coverage: 100%)
Gene names: ARID2, BAF200, KIAA1557
Sequence domains:
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 Chain: M
Molecule details ›
Chain: M
Length: 385 amino acids
Theoretical weight: 44.2 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q12824 (Residues: 1-385; Coverage: 100%)
Gene names: BAF47, INI1, SMARCB1, SNF5L1
Sequence domains:
SWI/SNF complex subunit SMARCC2 Chains: N, O
Molecule details ›
Chains: N, O
Length: 1214 amino acids
Theoretical weight: 133.05 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q8TAQ2 (Residues: 1-1214; Coverage: 100%)
Gene names: BAF170, SMARCC2
Sequence domains:
Unknown Chain: a
Molecule details ›
Chain: a
Length: 12 amino acids
Theoretical weight: 1.04 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 Chain: P
Molecule details ›
Chain: P
Length: 515 amino acids
Theoretical weight: 58.31 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q96GM5 (Residues: 1-515; Coverage: 100%)
Gene names: BAF60A, SMARCD1
Sequence domains: SWIB/MDM2 domain
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 Chain: Q
Molecule details ›
Chain: Q
Length: 411 amino acids
Theoretical weight: 46.71 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q969G3 (Residues: 1-411; Coverage: 100%)
Gene names: BAF57, SMARCE1
Sequence domains: HMG (high mobility group) box
PHD finger protein 10 Chain: R
Molecule details ›
Chain: R
Length: 498 amino acids
Theoretical weight: 56.13 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q8WUB8 (Residues: 1-498; Coverage: 100%)
Gene names: BAF45A, PHF10
Sequence domains: PHD-finger
Bromodomain-containing protein 7 Chain: S
Molecule details ›
Chain: S
Length: 651 amino acids
Theoretical weight: 74.26 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9NPI1 (Residues: 1-651; Coverage: 100%)
Gene names: BP75, BRD7, CELTIX1
Sequence domains:
Unkown Chain: T
Molecule details ›
Chain: T
Length: 22 amino acids
Theoretical weight: 1.89 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Protein polybromo-1 Chain: U
Molecule details ›
Chain: U
Length: 1597 amino acids
Theoretical weight: 184.16 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q86U86 (Residues: 1-513, 514-1689; Coverage: 94%)
Gene names: BAF180, PB1, PBRM1
Sequence domains:
Unknown Chain: V
Molecule details ›
Chain: V
Length: 102 amino acids
Theoretical weight: 8.7 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Unknown Chain: W
Molecule details ›
Chain: W
Length: 24 amino acids
Theoretical weight: 2.06 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
DNA (213-MER) Chain: X
Molecule details ›
Chain: X
Length: 213 nucleotides
Theoretical weight: 65.53 KDa
DNA (213-MER) Chain: Y
Molecule details ›
Chain: Y
Length: 213 nucleotides
Theoretical weight: 66 KDa

Ligands and Environments

3 bound ligands:
Ligand ADP 1 x ADP
Ligand MG 1 x MG
Ligand BEF 1 x BEF
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.4Å
Relevant EMDB volumes: EMD-33684
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Homo sapiens

Quick links

Citations

1 review citation

Epigenetic Regulation of Fibroblasts and Crosstalk between Cardiomyocytes and Non-Myocyte Cells in Cardiac Fibrosis.
Chu et al. (2023)
2 other articles