› › Structure analysis

Composite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome

Electron Microscopy
3.1Å resolution
PDB entry 8hy0 coloured by chain, front view.
PDB entry 8hy0 coloured by chain, side view.
PDB entry 8hy0 coloured by chain, top view.
Source organisms:
Assembly composition:
hetero hexadecamer (preferred)
Entry contents: 8 distinct polypeptide molecules
2 distinct DNA molecules

Quick links

Assemblies

Assembly 1 (preferred)
Download    3D Visualisation
Multimeric state: hetero hexadecamer
Accessible surface area: 164476.72 Å2
Buried surface area: 100473.96 Å2
Dissociation area: 2,627.03 Å2
Dissociation energy (ΔGdiss): 26.45 kcal/mol
Dissociation entropy (TΔSdiss): 13.7 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-270506

Macromolecules

Histone H3.2
Chains: 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 in PDB entry 8hy0, assembly 1, front view.
Histone H3 in PDB entry 8hy0, assembly 1, side view.
Histone H3 in PDB entry 8hy0, assembly 1, top view.
Molecule details ›

Search similar proteins

Histone H4
Chains: 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 8hy0, assembly 1, front view.
Histone H4 in PDB entry 8hy0, assembly 1, side view.
Histone H4 in PDB entry 8hy0, assembly 1, top view.
Molecule details ›

Search similar proteins

Histone H2A type 1
Chains: 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 in PDB entry 8hy0, assembly 1, front view.
Histone H2A in PDB entry 8hy0, assembly 1, side view.
Histone H2A in PDB entry 8hy0, assembly 1, top view.
Molecule details ›

Search similar proteins

Histone H2B 1.1
Chains: 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 in PDB entry 8hy0, assembly 1, front view.
Histone H2B in PDB entry 8hy0, assembly 1, side view.
Histone H2B in PDB entry 8hy0, assembly 1, top view.
Molecule details ›

Search similar proteins

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 8hy0, assembly 1, front view.
Transcriptional regulatory protein SIN3 in PDB entry 8hy0, assembly 1, side view.
Transcriptional regulatory protein SIN3 in PDB entry 8hy0, assembly 1, top view.
Molecule details ›

Search similar proteins

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 8hy0, assembly 1, front view.
Histone deacetylase RPD3 in PDB entry 8hy0, assembly 1, side view.
Histone deacetylase RPD3 in PDB entry 8hy0, assembly 1, top view.
Molecule details ›

Search similar proteins

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 8hy0, assembly 1, front view.
Chromatin modification-related protein EAF3 in PDB entry 8hy0, assembly 1, side view.
Chromatin modification-related protein EAF3 in PDB entry 8hy0, assembly 1, top view.
Molecule details ›

Search similar proteins

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
PHD-type domain-containing protein in PDB entry 8hy0, assembly 1, front view.
PHD-type domain-containing protein in PDB entry 8hy0, assembly 1, side view.
PHD-type domain-containing protein in PDB entry 8hy0, assembly 1, top view.
Molecule details ›

Search similar proteins

DNA chain I
Name: DNA (352-MER)
Representative chains: I
Length: 352 nucleotides
Theoretical weight: 108.34 KDa
DNA (352-MER) in PDB entry 8hy0, assembly 1, front view.
DNA (352-MER) in PDB entry 8hy0, assembly 1, side view.
DNA (352-MER) in PDB entry 8hy0, assembly 1, top view.
Molecule details ›

Search similar DNA

DNA chain J
Name: DNA (352-MER)
Representative chains: J
Length: 352 nucleotides
Theoretical weight: 109.08 KDa
DNA (352-MER) in PDB entry 8hy0, assembly 1, front view.
DNA (352-MER) in PDB entry 8hy0, assembly 1, side view.
DNA (352-MER) in PDB entry 8hy0, assembly 1, top view.
Molecule details ›

Search similar DNA

Quick links