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Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome

Electron Microscopy
7.6Å resolution
PDB entry 8jho coloured by chain, front view.
PDB entry 8jho coloured by chain, side view.
PDB entry 8jho coloured by chain, top view.
Source organisms:
Assembly composition:
hetero 24-mer (preferred)
Entry contents: 8 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 24-mer
Accessible surface area: 252224.91 Å2
Buried surface area: 160902.04 Å2
Dissociation area: 3,964.48 Å2
Dissociation energy (ΔGdiss): 47.26 kcal/mol
Dissociation entropy (TΔSdiss): 16.65 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-270551

Macromolecules

Histone H3.2
Chains: A, E, a, e
Length: 135 amino acids
Theoretical weight: 15.33 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 2-136; Coverage: 99%)
Pfam: Core histone H2A/H2B/H3/H4
Histone H3.2 in PDB entry 8jho, assembly 1, front view.
Histone H3.2 in PDB entry 8jho, assembly 1, side view.
Histone H3.2 in PDB entry 8jho, assembly 1, top view.
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Histone H4
Chains: B, F, b, f
Length: 102 amino acids
Theoretical weight: 11.26 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 2-103; Coverage: 99%)
Pfam: Centromere kinetochore component CENP-T histone fold
Histone H4 in PDB entry 8jho, assembly 1, front view.
Histone H4 in PDB entry 8jho, assembly 1, side view.
Histone H4 in PDB entry 8jho, assembly 1, top view.
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Histone H2A type 1
Chains: C, G, c, g
Length: 129 amino acids
Theoretical weight: 13.98 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 2-130; Coverage: 99%)
Pfam:
Histone H2A type 1 in PDB entry 8jho, assembly 1, front view.
Histone H2A type 1 in PDB entry 8jho, assembly 1, side view.
Histone H2A type 1 in PDB entry 8jho, assembly 1, top view.
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Histone H2B 1.1
Chains: D, H, d, h
Length: 122 amino acids
Theoretical weight: 13.52 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
Pfam: Core histone H2A/H2B/H3/H4
Histone H2B 1.1 in PDB entry 8jho, assembly 1, front view.
Histone H2B 1.1 in PDB entry 8jho, assembly 1, side view.
Histone H2B 1.1 in PDB entry 8jho, assembly 1, top view.
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Transcriptional regulatory protein SIN3
Chain: K
Length: 1536 amino acids
Theoretical weight: 175.05 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
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 8jho, assembly 1, front view.
Transcriptional regulatory protein SIN3 in PDB entry 8jho, assembly 1, side view.
Transcriptional regulatory protein SIN3 in PDB entry 8jho, assembly 1, top view.
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Histone deacetylase RPD3
Chain: L
Length: 433 amino acids
Theoretical weight: 48.96 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
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 8jho, assembly 1, front view.
Histone deacetylase RPD3 in PDB entry 8jho, assembly 1, side view.
Histone deacetylase RPD3 in PDB entry 8jho, assembly 1, top view.
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Chromatin modification-related protein EAF3
Chains: M, O
Length: 401 amino acids
Theoretical weight: 45.27 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q12432 (Residues: 1-401; Coverage: 100%)
Gene names: EAF3, YP9367.03C, YPR023C
Pfam:
Chromatin modification-related protein EAF3 in PDB entry 8jho, assembly 1, front view.
Chromatin modification-related protein EAF3 in PDB entry 8jho, assembly 1, side view.
Chromatin modification-related protein EAF3 in PDB entry 8jho, assembly 1, top view.
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Transcriptional regulatory protein RCO1
Chains: N, P
Length: 684 amino acids
Theoretical weight: 78.95 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q04779 (Residues: 1-684; Coverage: 100%)
Gene names: RCO1, YM9916.14, YMR075W
Pfam: PHD-finger
Transcriptional regulatory protein RCO1 in PDB entry 8jho, assembly 1, front view.
Transcriptional regulatory protein RCO1 in PDB entry 8jho, assembly 1, side view.
Transcriptional regulatory protein RCO1 in PDB entry 8jho, assembly 1, top view.
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DNA chain I
Name: Di-nucleosome template foward
Representative chains: I
Length: 350 nucleotides
Theoretical weight: 107.7 KDa
Di-nucleosome template foward in PDB entry 8jho, assembly 1, front view.
Di-nucleosome template foward in PDB entry 8jho, assembly 1, side view.
Di-nucleosome template foward in PDB entry 8jho, assembly 1, top view.
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DNA chain J
Name: Di-nucleosome template reverse
Representative chains: J
Length: 350 nucleotides
Theoretical weight: 108.49 KDa
Di-nucleosome template reverse in PDB entry 8jho, assembly 1, front view.
Di-nucleosome template reverse in PDB entry 8jho, assembly 1, side view.
Di-nucleosome template reverse in PDB entry 8jho, assembly 1, top view.
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