8w9d

Electron Microscopy
3.9Å resolution

Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1

Released:
Primary publication:
Structures and dynamics of Rpd3S complex bound to nucleosome.
OpenAccess logo Sci Adv 10 eadk7678 (2024)
PMID: 38598631
Related structures: EMD-37365

Function and Biology Details

Reaction catalysed:
Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
PDBe Complex ID:
PDB-CPX-270961 (preferred)
Entry contents:
9 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (11 distinct):
Transcriptional regulatory protein SIN3 Chain: A
Molecule details ›
Chain: A
Length: 1536 amino acids
Theoretical weight: 175.05 KDa
Source organism: Saccharomyces cerevisiae
Transcriptional regulatory protein RCO1 Chains: E, F
Molecule details ›
Chains: E, F
Length: 684 amino acids
Theoretical weight: 78.95 KDa
Source organism: Saccharomyces cerevisiae
Histone deacetylase RPD3 Chain: B
Molecule details ›
Chain: B
Length: 433 amino acids
Theoretical weight: 48.96 KDa
Source organism: Saccharomyces cerevisiae
Chromatin modification-related protein EAF3 Chains: C, D, G
Molecule details ›
Chains: C, D, G
Length: 401 amino acids
Theoretical weight: 45.27 KDa
Source organism: Saccharomyces cerevisiae
Histone H3.1 Chains: a, e
Molecule details ›
Chains: a, e
Length: 136 amino acids
Theoretical weight: 15.44 KDa
Source organism: Homo sapiens
Histone H4 Chains: b, f
Molecule details ›
Chains: b, f
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Homo sapiens
Histone H2A type 1-B/E Chains: c, g
Molecule details ›
Chains: c, g
Length: 130 amino acids
Theoretical weight: 14.17 KDa
Source organism: Homo sapiens
Histone H2B type 1-K Chains: d, h
Molecule details ›
Chains: d, h
Length: 126 amino acids
Theoretical weight: 13.92 KDa
Source organism: Homo sapiens
Unclear peptide Chain: H
Molecule details ›
Chain: H
Length: 5 amino acids
Theoretical weight: 488 Da
Source organism: Saccharomyces cerevisiae
5-DNA Chain: i
Molecule details ›
Chain: i
Length: 147 nucleotides
Theoretical weight: 45.37 KDa
Source organism: Homo sapiens
3-DNA Chain: j
Molecule details ›
Chain: j
Length: 147 nucleotides
Theoretical weight: 45.36 KDa
Source organism: Homo sapiens

Ligands and Environments

2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-37365