› 6uxw

Electron Microscopy
8.96Å resolution

SWI/SNF nucleosome complex with ADP-BeFx

Released:
DOI: 10.2210/pdb6uxw/pdb
PDB entry 6uxw coloured by chain, front view.
PDB entry 6uxw coloured by chain, side view.
PDB entry 6uxw coloured by chain, top view.
Source organisms:
Primary publication:
Cryo-EM structure of SWI/SNF complex bound to a nucleosome.
Han Y, Reyes AA, Malik S, He Y
Nature 579 452-455 (2020)
PMID: 32188938
Related structures: EMD-20934

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 28-mer (preferred)
PDBe Complex ID:
PDB-CPX-120739 (preferred)
Entry contents:
15 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (17 distinct):
Histone H3.2 Chains: R, V
Molecule details ›
Chains: R, V
Length: 135 amino acids
Theoretical weight: 15.3 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 2-136; Coverage: 99%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: S, W
Molecule details ›
Chains: S, W
Length: 102 amino acids
Theoretical weight: 11.26 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 2-103; Coverage: 99%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1 Chains: T, X
Molecule details ›
Chains: T, X
Length: 129 amino acids
Theoretical weight: 13.98 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 2-130; Coverage: 99%)
Sequence domains:
Histone H2B 1.1 Chains: U, Y
Molecule details ›
Chains: U, Y
Length: 122 amino acids
Theoretical weight: 13.52 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
Sequence domains: Core histone H2A/H2B/H3/H4
Actin-related protein 7 Chain: P
Molecule details ›
Chain: P
Length: 477 amino acids
Theoretical weight: 53.86 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q12406 (Residues: 1-477; Coverage: 100%)
Gene names: ARP7, SWP61, YP9367.14, YPR034W
Sequence domains: Actin
Actin-like protein ARP9 Chain: Q
Molecule details ›
Chain: Q
Length: 467 amino acids
Theoretical weight: 53.13 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q05123 (Residues: 1-467; Coverage: 100%)
Gene names: ARP9, SWP59, YM9973.07, YMR033W
Sequence domains: Actin
Regulator of Ty1 transposition protein 102 Chain: Z
Molecule details ›
Chain: Z
Length: 157 amino acids
Theoretical weight: 17.82 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53330 (Residues: 1-157; Coverage: 100%)
Gene names: G9378, RTT102, YGR275W
Sequence domains: Rtt102p-like transcription regulator protein
Transcription regulatory protein SNF2 Chain: A
Molecule details ›
Chain: A
Length: 1703 amino acids
Theoretical weight: 194.32 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P22082 (Residues: 1-1703; Coverage: 100%)
Gene names: GAM1, RIC1, SNF2, SWI2, TYE3, YOR290C
Sequence domains:
SWI/SNF chromatin-remodeling complex subunit SWI1 Chain: B
Molecule details ›
Chain: B
Length: 1314 amino acids
Theoretical weight: 148.07 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P09547 (Residues: 1-1314; Coverage: 100%)
Gene names: ADR6, GAM3, LPA1, SWI1, YPL016W
Sequence domains: ARID/BRIGHT DNA binding domain
SWI/SNF chromatin-remodeling complex subunit SNF5 Chain: C
Molecule details ›
Chain: C
Length: 905 amino acids
Theoretical weight: 102.64 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P18480 (Residues: 1-905; Coverage: 100%)
Gene names: SNF5, SWI10, TYE4, YBR2036, YBR289W
Sequence domains: SNF5 / SMARCB1 / INI1
SWI/SNF complex subunit SWI3 Chains: D, E, F, G
Molecule details ›
Chains: D, E, F, G
Length: 825 amino acids
Theoretical weight: 93.03 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32591 (Residues: 1-825; Coverage: 100%)
Gene names: J0495, SWI3, TYE2, YJL176C
Sequence domains:
Transcription regulatory protein SNF12 Chain: H
Molecule details ›
Chain: H
Length: 566 amino acids
Theoretical weight: 63.95 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53628 (Residues: 1-566; Coverage: 100%)
Gene names: N3224, SNF12, SWP73, YNR023W
Transcription regulatory protein SNF6 Chain: I
Molecule details ›
Chain: I
Length: 179 amino acids
Theoretical weight: 19.57 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P18888 (Residues: 1-150; Coverage: 45%)
Gene names: SNF6, YHL025W
Unknown protein Chains: J, K, L, N, O
Molecule details ›
Chains: J, K, L, N, O
Length: 67 amino acids
Theoretical weight: 5.72 KDa
Source organism: Saccharomyces cerevisiae S288C
SWI/SNF global transcription activator complex subunit SWP82 Chain: M
Molecule details ›
Chain: M
Length: 83 amino acids
Theoretical weight: 7.08 KDa
Source organism: Saccharomyces cerevisiae S288C
601 sequence bottom strand Chain: a
Molecule details ›
Chain: a
Length: 185 nucleotides
Theoretical weight: 56.94 KDa
601 sequence top strand Chain: b
Molecule details ›
Chain: b
Length: 200 nucleotides
Theoretical weight: 61.79 KDa

Ligands and Environments

4 bound ligands:
Ligand PO4 12 x PO4
Ligand ADP 1 x ADP
Ligand BEF 1 x BEF
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 8.96Å
Relevant EMDB volumes: EMD-20934
Expression system: Escherichia coli

Quick links

Citations

15 review citations

Epigenetic regulation in metabolic diseases: mechanisms and advances in clinical study.
Wu et al. (2023)
14 more

11 mentions without citation

Structure and Function of Chromatin Remodelers.
Reyes et al. (2021)
10 more