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The ClassB RSC-Nucleosome Complex

Electron Microscopy
7.55Å resolution
PDB entry 6kw4 coloured by chain, front view.
PDB entry 6kw4 coloured by chain, side view.
PDB entry 6kw4 coloured by chain, top view.
Source organisms:
Assembly composition:
hetero 28-mer (preferred)
Entry contents: 19 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 28-mer
Accessible surface area: 253165.32 Å2
Buried surface area: 167132.4 Å2
Dissociation area: 49.46 Å2
Dissociation energy (ΔGdiss): -37.06 kcal/mol
Dissociation entropy (TΔSdiss): 34.73 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-120179

Macromolecules

Histone H3.2
Chains: N, Q
Length: 136 amino acids
Theoretical weight: 15.42 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 1-136; Coverage: 100%)
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
Histone H3.2 in PDB entry 6kw4, assembly 1, front view.
Histone H3.2 in PDB entry 6kw4, assembly 1, side view.
Histone H3.2 in PDB entry 6kw4, assembly 1, top view.
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Histone H4
Chains: B, R
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
Pfam: Centromere kinetochore component CENP-T histone fold
InterPro:
Histone H4 in PDB entry 6kw4, assembly 1, front view.
Histone H4 in PDB entry 6kw4, assembly 1, side view.
Histone H4 in PDB entry 6kw4, assembly 1, top view.
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Histone H2A type 1
Chains: O, S
Length: 130 amino acids
Theoretical weight: 14.11 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 1-130; Coverage: 100%)
Pfam:
InterPro:
Histone H2A type 1 in PDB entry 6kw4, assembly 1, front view.
Histone H2A type 1 in PDB entry 6kw4, assembly 1, side view.
Histone H2A type 1 in PDB entry 6kw4, assembly 1, top view.
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Actin-related protein 7
Chain: f
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
Pfam: Actin
InterPro:
Actin-related protein 7 in PDB entry 6kw4, assembly 1, front view.
Actin-related protein 7 in PDB entry 6kw4, assembly 1, side view.
Actin-related protein 7 in PDB entry 6kw4, assembly 1, top view.
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Regulator of Ty1 transposition protein 102
Chain: h
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
Pfam: Rtt102p-like transcription regulator protein
InterPro: Transcription regulator protein Rtt102
Regulator of Ty1 transposition protein 102 in PDB entry 6kw4, assembly 1, front view.
Regulator of Ty1 transposition protein 102 in PDB entry 6kw4, assembly 1, side view.
Regulator of Ty1 transposition protein 102 in PDB entry 6kw4, assembly 1, top view.
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Chromatin structure-remodeling complex subunit RSC7
Chain: F
Length: 435 amino acids
Theoretical weight: 49.72 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32832 (Residues: 1-435; Coverage: 100%)
Gene names: NPL6, RSC7, YM9582.16C, YMR091C
Pfam: Chromatin remodelling complex Rsc7/Swp82 subunit
InterPro: Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82
Chromatin structure-remodeling complex subunit RSC7 in PDB entry 6kw4, assembly 1, front view.
Chromatin structure-remodeling complex subunit RSC7 in PDB entry 6kw4, assembly 1, side view.
Chromatin structure-remodeling complex subunit RSC7 in PDB entry 6kw4, assembly 1, top view.
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Chromatin structure-remodeling complex protein RSC8
Chains: D, H
Length: 557 amino acids
Theoretical weight: 63.25 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P43609 (Residues: 1-557; Coverage: 100%)
Gene names: RSC8, SWH3, YFR037C
Pfam:
InterPro:
Chromatin structure-remodeling complex protein RSC8 in PDB entry 6kw4, assembly 1, front view.
Chromatin structure-remodeling complex protein RSC8 in PDB entry 6kw4, assembly 1, side view.
Chromatin structure-remodeling complex protein RSC8 in PDB entry 6kw4, assembly 1, top view.
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Chromatin structure-remodeling complex subunit RSC9
Chain: M
Length: 581 amino acids
Theoretical weight: 65.29 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q03124 (Residues: 1-581; Coverage: 100%)
Gene names: RSC9, YM4987.08, YML127W
InterPro: DNA-binding RFX-type winged-helix domain
Chromatin structure-remodeling complex subunit RSC9 in PDB entry 6kw4, assembly 1, front view.
Chromatin structure-remodeling complex subunit RSC9 in PDB entry 6kw4, assembly 1, side view.
Chromatin structure-remodeling complex subunit RSC9 in PDB entry 6kw4, assembly 1, top view.
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Chromatin structure-remodeling complex protein RSC6
Chain: I
Length: 483 amino acids
Theoretical weight: 54.22 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25632 (Residues: 1-483; Coverage: 100%)
Gene names: RSC6, YCR052W, YCR52W
InterPro: SWIB/MDM2 domain superfamily
Chromatin structure-remodeling complex protein RSC6 in PDB entry 6kw4, assembly 1, front view.
Chromatin structure-remodeling complex protein RSC6 in PDB entry 6kw4, assembly 1, side view.
Chromatin structure-remodeling complex protein RSC6 in PDB entry 6kw4, assembly 1, top view.
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Chromatin structure-remodeling complex subunit SFH1
Chain: G
Length: 426 amino acids
Theoretical weight: 48.83 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06168 (Residues: 1-426; Coverage: 100%)
Gene names: L8543.4, SFH1, YLR321C
Pfam: SNF5 / SMARCB1 / INI1
InterPro:
Chromatin structure-remodeling complex subunit SFH1 in PDB entry 6kw4, assembly 1, front view.
Chromatin structure-remodeling complex subunit SFH1 in PDB entry 6kw4, assembly 1, side view.
Chromatin structure-remodeling complex subunit SFH1 in PDB entry 6kw4, assembly 1, top view.
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Chromatin structure-remodeling complex protein RSC58
Chain: A
Length: 502 amino acids
Theoretical weight: 57.87 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q07979 (Residues: 1-502; Coverage: 100%)
Gene names: RSC58, YLR033W
Pfam: Bromodomain
InterPro:
Chromatin structure-remodeling complex protein RSC58 in PDB entry 6kw4, assembly 1, front view.
Chromatin structure-remodeling complex protein RSC58 in PDB entry 6kw4, assembly 1, side view.
Chromatin structure-remodeling complex protein RSC58 in PDB entry 6kw4, assembly 1, top view.
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Nuclear protein STH1/NPS1
Chains: J, V, Y
Length: 1359 amino acids
Theoretical weight: 156.98 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32597 (Residues: 1-1359; Coverage: 100%)
Gene names: NPS1, STH1, YIL126W
Pfam:
InterPro:
Nuclear protein STH1/NPS1 in PDB entry 6kw4, assembly 1, front view.
Nuclear protein STH1/NPS1 in PDB entry 6kw4, assembly 1, side view.
Nuclear protein STH1/NPS1 in PDB entry 6kw4, assembly 1, top view.
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High temperature lethal protein 1
Chain: E
Length: 78 amino acids
Theoretical weight: 9.19 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q9URQ5 (Residues: 1-78; Coverage: 100%)
Gene names: DRT1, HTL1, YCR020W-B
High temperature lethal protein 1 in PDB entry 6kw4, assembly 1, front view.
High temperature lethal protein 1 in PDB entry 6kw4, assembly 1, side view.
High temperature lethal protein 1 in PDB entry 6kw4, assembly 1, top view.
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Chromatin structure-remodeling complex protein RSC30
Chain: C
Length: 883 amino acids
Theoretical weight: 101.45 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38781 (Residues: 1-883; Coverage: 100%)
Gene names: RSC30, YHR056C
Pfam: Fungal Zn(2)-Cys(6) binuclear cluster domain
InterPro:
Chromatin structure-remodeling complex protein RSC30 in PDB entry 6kw4, assembly 1, front view.
Chromatin structure-remodeling complex protein RSC30 in PDB entry 6kw4, assembly 1, side view.
Chromatin structure-remodeling complex protein RSC30 in PDB entry 6kw4, assembly 1, top view.
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Chromatin structure-remodeling complex protein RSC3
Chain: K
Length: 885 amino acids
Theoretical weight: 101.83 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06639 (Residues: 1-885; Coverage: 100%)
Gene names: D9740.13, RSC3, YDR303C
Pfam: Fungal Zn(2)-Cys(6) binuclear cluster domain
InterPro:
Chromatin structure-remodeling complex protein RSC3 in PDB entry 6kw4, assembly 1, front view.
Chromatin structure-remodeling complex protein RSC3 in PDB entry 6kw4, assembly 1, side view.
Chromatin structure-remodeling complex protein RSC3 in PDB entry 6kw4, assembly 1, top view.
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Chromatin structure-remodeling complex subunit RSC4
Chain: X
Length: 625 amino acids
Theoretical weight: 72.37 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q02206 (Residues: 1-625; Coverage: 100%)
Gene names: RSC4, YK107, YKR008W
Pfam: Bromodomain
InterPro:
Chromatin structure-remodeling complex subunit RSC4 in PDB entry 6kw4, assembly 1, front view.
Chromatin structure-remodeling complex subunit RSC4 in PDB entry 6kw4, assembly 1, side view.
Chromatin structure-remodeling complex subunit RSC4 in PDB entry 6kw4, assembly 1, top view.
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Chromatin structure-remodeling complex subunit RSC2
Chain: L
Length: 889 amino acids
Theoretical weight: 102.44 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06488 (Residues: 1-889; Coverage: 100%)
Gene names: L9638.1, RSC2, YLR357W
Pfam:
InterPro:
Chromatin structure-remodeling complex subunit RSC2 in PDB entry 6kw4, assembly 1, front view.
Chromatin structure-remodeling complex subunit RSC2 in PDB entry 6kw4, assembly 1, side view.
Chromatin structure-remodeling complex subunit RSC2 in PDB entry 6kw4, assembly 1, top view.
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Histone H2B 1.1
Chains: P, T
Length: 126 amino acids
Theoretical weight: 13.93 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 1-126; Coverage: 100%)
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
Histone H2B 1.1 in PDB entry 6kw4, assembly 1, front view.
Histone H2B 1.1 in PDB entry 6kw4, assembly 1, side view.
Histone H2B 1.1 in PDB entry 6kw4, assembly 1, top view.
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Actin-like protein ARP9
Chain: g
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
Pfam: Actin
InterPro:
Actin-like protein ARP9 in PDB entry 6kw4, assembly 1, front view.
Actin-like protein ARP9 in PDB entry 6kw4, assembly 1, side view.
Actin-like protein ARP9 in PDB entry 6kw4, assembly 1, top view.
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DNA chain U
Name: DNA 167
Representative chains: U
Length: 167 nucleotides
Theoretical weight: 51.42 KDa
DNA 167 in PDB entry 6kw4, assembly 1, front view.
DNA 167 in PDB entry 6kw4, assembly 1, side view.
DNA 167 in PDB entry 6kw4, assembly 1, top view.
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DNA chain W
Name: DNA 167
Representative chains: W
Length: 167 nucleotides
Theoretical weight: 51.68 KDa
DNA 167 in PDB entry 6kw4, assembly 1, front view.
DNA 167 in PDB entry 6kw4, assembly 1, side view.
DNA 167 in PDB entry 6kw4, assembly 1, top view.
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