› 9fbw

Electron Microscopy
4.4Å resolution

SWR1 lacking Swc5 subunit in complex with hexasome

Released:
DOI: 10.2210/pdb9fbw/pdb
PDB entry 9fbw coloured by chain, front view.
PDB entry 9fbw coloured by chain, side view.
PDB entry 9fbw coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Stabilization of the hexasome intermediate during histone exchange by yeast SWR1 complex.
Jalal ASB, Girvan P, Chua EYD, Liu L, Wang S, McCormack EA, Skehan MT, Knight CL, Rueda DS, Wigley DB
Mol Cell (2024)
PMID: 39226902
Related structures: EMD-50297

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
PDBe Complex ID:
PDB-CPX-271071 (preferred)
Entry contents:
10 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (12 distinct):
Histone H3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 136 amino acids
Theoretical weight: 15.41 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P61830 (Residues: 1-136; Coverage: 100%)
Gene names: HHT1, HHT2, N2749, SIN2, YBR010W, YBR0201, YNL031C
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: C, D
Molecule details ›
Chains: C, D
Length: 103 amino acids
Theoretical weight: 11.4 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P02309 (Residues: 1-103; Coverage: 100%)
Gene names: HHF1, HHF2, N2752, YBR009C, YBR0122, YNL030W
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A.1 Chain: E
Molecule details ›
Chain: E
Length: 132 amino acids
Theoretical weight: 14.01 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P04911 (Residues: 1-132; Coverage: 100%)
Gene names: H2A1, HTA1, SPT11, YD9934.10, YDR225W
Sequence domains:
Histone H2B.1 Chain: G
Molecule details ›
Chain: G
Length: 131 amino acids
Theoretical weight: 14.28 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P02293 (Residues: 1-131; Coverage: 100%)
Gene names: H2B1, HTB1, SPT12, YD9934.09C, YDR224C
Sequence domains: Core histone H2A/H2B/H3/H4
Helicase SWR1 Chain: M
Molecule details ›
Chain: M
Length: 1514 amino acids
Theoretical weight: 174.79 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q05471 (Residues: 1-1514; Coverage: 100%)
Gene names: D9651.6, SWR1, YDR334W
Sequence domains:
Actin-like protein ARP6 Chain: R
Molecule details ›
Chain: R
Length: 438 amino acids
Theoretical weight: 50.1 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q12509 (Residues: 1-438; Coverage: 100%)
Gene names: ARP6, L2393, L9449.13, YLR085C
Sequence domains: Actin
Vacuolar protein sorting-associated protein 71 Chain: S
Molecule details ›
Chain: S
Length: 280 amino acids
Theoretical weight: 32.07 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q03433 (Residues: 1-280; Coverage: 100%)
Gene names: SWC6, VPS71, YM8054.02C, YML041C
RuvB-like protein 1 Chains: T, V, X
Molecule details ›
Chains: T, V, X
Length: 463 amino acids
Theoretical weight: 50.52 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q03940 (Residues: 1-463; Coverage: 100%)
Gene names: RVB1, TIH1, TIP49A, YDR190C
Sequence domains:
RuvB-like protein 2 Chains: U, W, Y
Molecule details ›
Chains: U, W, Y
Length: 471 amino acids
Theoretical weight: 51.67 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q12464 (Residues: 1-471; Coverage: 100%)
Gene names: P1060, RVB2, TIH2, TIP49B, YPL235W
Sequence domains:
Vacuolar protein sorting-associated protein 72 Chain: Z
Molecule details ›
Chain: Z
Length: 795 amino acids
Theoretical weight: 90.71 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q03388 (Residues: 1-795; Coverage: 100%)
Gene names: SWC2, VPS72, YDR485C
Sequence domains:
DNA (112-MER) Chain: I
Molecule details ›
Chain: I
Length: 112 nucleotides
Theoretical weight: 34.36 KDa
DNA (112-MER) Chain: J
Molecule details ›
Chain: J
Length: 112 nucleotides
Theoretical weight: 34.76 KDa

Ligands and Environments

4 bound ligands:
Ligand ADP 8 x ADP
Ligand BEF 2 x BEF
Ligand MG 8 x MG
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.4Å
Relevant EMDB volumes: EMD-50297
Expression systems:
  • Escherichia coli
  • Trichoplusia ni

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