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Cryo-EM structure of Rpd3S in close-state Rpd3S-NCP complex

Electron Microscopy
3.3Å resolution
PDB entry 7yi3 coloured by chain, front view.
PDB entry 7yi3 coloured by chain, side view.
PDB entry 7yi3 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Assembly composition:
hetero pentamer (preferred)
Entry contents: 4 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero pentamer
Accessible surface area: 62674.53 Å2
Buried surface area: 24960.05 Å2
Dissociation area: 426.05 Å2
Dissociation energy (ΔGdiss): -5.42 kcal/mol
Dissociation entropy (TΔSdiss): 9.01 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-218077

Macromolecules

Transcriptional regulatory protein SIN3
Chain: A
Length: 1536 amino acids
Theoretical weight: 175.05 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P22579 (Residues: 1-1536; Coverage: 100%)
Gene names: CPE1, GAM2, RPD1, SDI1, SDS16, SIN3, UME4, YOL004W
Pfam:
Transcriptional regulatory protein SIN3 in PDB entry 7yi3, assembly 1, front view.
Transcriptional regulatory protein SIN3 in PDB entry 7yi3, assembly 1, side view.
Transcriptional regulatory protein SIN3 in PDB entry 7yi3, assembly 1, top view.
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Histone deacetylase RPD3
Chain: B
Length: 433 amino acids
Theoretical weight: 48.96 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P32561 (Residues: 1-433; Coverage: 100%)
Gene names: MOF6, N0305, REC3, RPD3, SDI2, SDS6, YNL330C
Pfam: Histone deacetylase domain
Histone deacetylase RPD3 in PDB entry 7yi3, assembly 1, front view.
Histone deacetylase RPD3 in PDB entry 7yi3, assembly 1, side view.
Histone deacetylase RPD3 in PDB entry 7yi3, assembly 1, top view.
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Chromatin modification-related protein EAF3
Chain: C
Length: 401 amino acids
Theoretical weight: 45.27 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q12432 (Residues: 1-401; Coverage: 100%)
Gene names: EAF3, YP9367.03C, YPR023C
Pfam:
Chromatin modification-related protein EAF3 in PDB entry 7yi3, assembly 1, front view.
Chromatin modification-related protein EAF3 in PDB entry 7yi3, assembly 1, side view.
Chromatin modification-related protein EAF3 in PDB entry 7yi3, assembly 1, top view.
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Transcriptional regulatory protein RCO1
Chains: D, E
Length: 684 amino acids
Theoretical weight: 78.95 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q04779 (Residues: 1-684; Coverage: 100%)
Gene names: RCO1, YM9916.14, YMR075W
Pfam: PHD-finger
Transcriptional regulatory protein RCO1 in PDB entry 7yi3, assembly 1, front view.
Transcriptional regulatory protein RCO1 in PDB entry 7yi3, assembly 1, side view.
Transcriptional regulatory protein RCO1 in PDB entry 7yi3, assembly 1, top view.
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