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

Electron Microscopy
3.4Å resolution
PDB entry 7yi2 coloured by chain, front view.
PDB entry 7yi2 coloured by chain, side view.
PDB entry 7yi2 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Assembly composition:
hetero heptamer (preferred)
Entry contents: 4 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero heptamer
Accessible surface area: 68410.02 Å2
Buried surface area: 27035.63 Å2
Dissociation area: 690.03 Å2
Dissociation energy (ΔGdiss): -14.03 kcal/mol
Dissociation entropy (TΔSdiss): 21.23 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-217985

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 7yi2, assembly 1, front view.
Transcriptional regulatory protein SIN3 in PDB entry 7yi2, assembly 1, side view.
Transcriptional regulatory protein SIN3 in PDB entry 7yi2, 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 7yi2, assembly 1, front view.
Histone deacetylase RPD3 in PDB entry 7yi2, assembly 1, side view.
Histone deacetylase RPD3 in PDB entry 7yi2, 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 7yi2, assembly 1, front view.
Chromatin modification-related protein EAF3 in PDB entry 7yi2, assembly 1, side view.
Chromatin modification-related protein EAF3 in PDB entry 7yi2, 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 7yi2, assembly 1, front view.
Transcriptional regulatory protein RCO1 in PDB entry 7yi2, assembly 1, side view.
Transcriptional regulatory protein RCO1 in PDB entry 7yi2, assembly 1, top view.
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DNA chain G
Name: Wisdom 601 DNA (167-MER)
Representative chains: G
Length: 167 nucleotides
Theoretical weight: 51.31 KDa
Wisdom 601 DNA (167-MER) in PDB entry 7yi2, assembly 1, front view.
Wisdom 601 DNA (167-MER) in PDB entry 7yi2, assembly 1, side view.
Wisdom 601 DNA (167-MER) in PDB entry 7yi2, assembly 1, top view.
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DNA chain H
Name: Wisdom 601 DNA (167-MER)
Representative chains: H
Length: 167 nucleotides
Theoretical weight: 51.8 KDa
Wisdom 601 DNA (167-MER) in PDB entry 7yi2, assembly 1, front view.
Wisdom 601 DNA (167-MER) in PDB entry 7yi2, assembly 1, side view.
Wisdom 601 DNA (167-MER) in PDB entry 7yi2, assembly 1, top view.
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