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Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1

Electron Microscopy
2.93Å resolution
PDB entry 8kd4 coloured by chain, front view.
PDB entry 8kd4 coloured by chain, side view.
PDB entry 8kd4 coloured by chain, top view.
Source organisms:
Assembly composition:
hetero hexadecamer (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 hexadecamer
Accessible surface area: 155321.9 Å2
Buried surface area: 92177.02 Å2
Dissociation area: 1,493.11 Å2
Dissociation energy (ΔGdiss): 6.39 kcal/mol
Dissociation entropy (TΔSdiss): 14.97 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-240146

Macromolecules

Chromatin modification-related protein EAF3
Chains: D, F
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 8kd4, assembly 1, front view.
Chromatin modification-related protein EAF3 in PDB entry 8kd4, assembly 1, side view.
Chromatin modification-related protein EAF3 in PDB entry 8kd4, assembly 1, top view.
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Histone H3.2
Chains: O, S
Length: 135 amino acids
Theoretical weight: 15.31 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 in PDB entry 8kd4, assembly 1, front view.
Histone H3 in PDB entry 8kd4, assembly 1, side view.
Histone H3 in PDB entry 8kd4, assembly 1, top view.
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Histone H4
Chains: P, T
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 8kd4, assembly 1, front view.
Histone H4 in PDB entry 8kd4, assembly 1, side view.
Histone H4 in PDB entry 8kd4, assembly 1, top view.
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Histone H2A type 1
Chains: Q, U
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 in PDB entry 8kd4, assembly 1, front view.
Histone H2A in PDB entry 8kd4, assembly 1, side view.
Histone H2A in PDB entry 8kd4, assembly 1, top view.
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Histone H2B 1.1
Chains: R, V
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 8kd4, assembly 1, front view.
Histone H2B 1.1 in PDB entry 8kd4, assembly 1, side view.
Histone H2B 1.1 in PDB entry 8kd4, assembly 1, top view.
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Histone deacetylase RPD3
Chain: A
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 8kd4, assembly 1, front view.
Histone deacetylase RPD3 in PDB entry 8kd4, assembly 1, side view.
Histone deacetylase RPD3 in PDB entry 8kd4, assembly 1, top view.
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Transcriptional regulatory protein SIN3
Chain: B
Length: 1371 amino acids
Theoretical weight: 157.59 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P22579 (Residues: 215-1536; Coverage: 86%)
Gene names: CPE1, GAM2, RPD1, SDI1, SDS16, SIN3, UME4, YOL004W
Pfam:
Transcriptional regulatory protein SIN3 in PDB entry 8kd4, assembly 1, front view.
Transcriptional regulatory protein SIN3 in PDB entry 8kd4, assembly 1, side view.
Transcriptional regulatory protein SIN3 in PDB entry 8kd4, assembly 1, top view.
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Transcriptional regulatory protein RCO1
Chains: E, G
Length: 733 amino acids
Theoretical weight: 84.47 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 8kd4, assembly 1, front view.
Transcriptional regulatory protein RCO1 in PDB entry 8kd4, assembly 1, side view.
Transcriptional regulatory protein RCO1 in PDB entry 8kd4, assembly 1, top view.
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DNA chain X
Name: 187bp DNA
Representative chains: X
Length: 187 nucleotides
Theoretical weight: 58.08 KDa
187bp DNA in PDB entry 8kd4, assembly 1, front view.
187bp DNA in PDB entry 8kd4, assembly 1, side view.
187bp DNA in PDB entry 8kd4, assembly 1, top view.
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DNA chain Y
Name: 187bp DNA
Representative chains: Y
Length: 187 nucleotides
Theoretical weight: 57.4 KDa
187bp DNA in PDB entry 8kd4, assembly 1, front view.
187bp DNA in PDB entry 8kd4, assembly 1, side view.
187bp DNA in PDB entry 8kd4, assembly 1, top view.
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