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Chromatin remodeller-nucleosome complex at 3.6 A resolution.

Electron Microscopy
3.6Å resolution
PDB entry 6gej coloured by chain, front view.
PDB entry 6gej coloured by chain, side view.
PDB entry 6gej coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Assembly composition:
hetero icosamer (preferred)
Entry contents: 10 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Nucleosome, variant HTA1-HTB1 and DNA
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Multimeric state: hetero icosamer
Accessible surface area: 254507.45 Å2
Buried surface area: 139747.23 Å2
Dissociation area: 1,951.46 Å2
Dissociation energy (ΔGdiss): 22.28 kcal/mol
Dissociation entropy (TΔSdiss): 13.8 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-119948

Macromolecules

Vacuolar protein sorting-associated protein 72
Chain: Z
Length: 131 amino acids
Theoretical weight: 11.17 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
Vacuolar protein sorting-associated protein 72 in PDB entry 6gej, assembly 1, front view.
Vacuolar protein sorting-associated protein 72 in PDB entry 6gej, assembly 1, side view.
Vacuolar protein sorting-associated protein 72 in PDB entry 6gej, assembly 1, top view.
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Histone H3
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
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
CATH: Histone, subunit A
Histone H3 in PDB entry 6gej, assembly 1, front view.
Histone H3 in PDB entry 6gej, assembly 1, side view.
Histone H3 in PDB entry 6gej, assembly 1, top view.
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Histone H4
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
Pfam: Centromere kinetochore component CENP-T histone fold
InterPro:
CATH: Histone, subunit A
Histone H4 in PDB entry 6gej, assembly 1, front view.
Histone H4 in PDB entry 6gej, assembly 1, side view.
Histone H4 in PDB entry 6gej, assembly 1, top view.
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Histone H2A.1
Chains: E, F
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
Pfam:
InterPro:
CATH: Histone, subunit A
Histone H2A.1 in PDB entry 6gej, assembly 1, front view.
Histone H2A.1 in PDB entry 6gej, assembly 1, side view.
Histone H2A.1 in PDB entry 6gej, assembly 1, top view.
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Histone H2B.1
Chains: G, H
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
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
CATH: Histone, subunit A
Histone H2B.1 in PDB entry 6gej, assembly 1, front view.
Histone H2B.1 in PDB entry 6gej, assembly 1, side view.
Histone H2B.1 in PDB entry 6gej, assembly 1, top view.
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Helicase SWR1
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
Pfam:
InterPro:
Helicase SWR1 in PDB entry 6gej, assembly 1, front view.
Helicase SWR1 in PDB entry 6gej, assembly 1, side view.
Helicase SWR1 in PDB entry 6gej, assembly 1, top view.
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Actin-like protein ARP6
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
Pfam: Actin
InterPro:
Actin-like protein ARP6 in PDB entry 6gej, assembly 1, front view.
Actin-like protein ARP6 in PDB entry 6gej, assembly 1, side view.
Actin-like protein ARP6 in PDB entry 6gej, assembly 1, top view.
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Vacuolar protein sorting-associated protein 71
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
InterPro:
Vacuolar protein sorting-associated protein 71 in PDB entry 6gej, assembly 1, front view.
Vacuolar protein sorting-associated protein 71 in PDB entry 6gej, assembly 1, side view.
Vacuolar protein sorting-associated protein 71 in PDB entry 6gej, assembly 1, top view.
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RuvB-like protein 1
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
Pfam:
InterPro:
RuvB-like protein 1 in PDB entry 6gej, assembly 1, front view.
RuvB-like protein 1 in PDB entry 6gej, assembly 1, side view.
RuvB-like protein 1 in PDB entry 6gej, assembly 1, top view.
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RuvB-like protein 2
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
Pfam:
InterPro:
RuvB-like protein 2 in PDB entry 6gej, assembly 1, front view.
RuvB-like protein 2 in PDB entry 6gej, assembly 1, side view.
RuvB-like protein 2 in PDB entry 6gej, assembly 1, top view.
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DNA chain I
Name: DNA (154-MER)
Representative chains: I
Length: 154 nucleotides
Theoretical weight: 47.27 KDa
DNA (154-MER) in PDB entry 6gej, assembly 1, front view.
DNA (154-MER) in PDB entry 6gej, assembly 1, side view.
DNA (154-MER) in PDB entry 6gej, assembly 1, top view.
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DNA chain J
Name: DNA (154-MER)
Representative chains: J
Length: 154 nucleotides
Theoretical weight: 47.8 KDa
DNA (154-MER) in PDB entry 6gej, assembly 1, front view.
DNA (154-MER) in PDB entry 6gej, assembly 1, side view.
DNA (154-MER) in PDB entry 6gej, assembly 1, top view.
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