› 8w9d

Electron Microscopy
3.9Å resolution

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

Released:
DOI: 10.2210/pdb8w9d/pdb
PDB entry 8w9d coloured by chain, front view.
PDB entry 8w9d coloured by chain, side view.
PDB entry 8w9d coloured by chain, top view.
Source organisms:
Primary publication:
Structures and dynamics of Rpd3S complex bound to nucleosome.
Wang C, Chu C, Guo Z, Zhan X
Sci Adv 10 eadk7678 (2024)
PMID: 38598631
Related structures: EMD-37365

Function and Biology Details

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-244359 (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
UniProt:
  • Best match: P22579 (Residues: 1-1536)
Gene names: CPE1, GAM2, RPD1, SDI1, SDS16, SIN3, UME4, YOL004W
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
UniProt:
  • Best match: Q04779 (Residues: 1-684)
Gene names: RCO1, YM9916.14, YMR075W
Histone deacetylase RPD3 Chain: B
Molecule details ›
Chain: B
Length: 433 amino acids
Theoretical weight: 48.96 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Best match: P32561 (Residues: 1-433)
Gene names: MOF6, N0305, REC3, RPD3, SDI2, SDS6, YNL330C
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
UniProt:
  • Best match: Q12432 (Residues: 1-401)
Gene names: EAF3, YP9367.03C, YPR023C
Histone H3.1 Chains: a, e
Molecule details ›
Chains: a, e
Length: 136 amino acids
Theoretical weight: 15.44 KDa
Source organism: Homo sapiens
UniProt:
  • Best match: P68431 (Residues: 1-136)
Gene names: H3C1, H3C10, H3C11, H3C12, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3FA, H3FB, H3FC HIST1H3C, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J
Histone H4 Chains: b, f
Molecule details ›
Chains: b, f
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Homo sapiens
UniProt:
  • Best match: P62805 (Residues: 1-103)
Gene names: H4-16, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4C1, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4
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
UniProt:
  • Best match: P04908 (Residues: 1-130)
Gene names: H2AC4, H2AC8, H2AFA, H2AFM, HIST1H2AB, HIST1H2AE
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
UniProt:
  • Best match: O60814 (Residues: 1-126)
Gene names: H2BC12, H2BFT, HIRIP1, HIST1H2BK
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
3-DNA Chain: j
Molecule details ›
Chain: j
Length: 147 nucleotides
Theoretical weight: 45.36 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 7 x ZN
Ligand K 2 x K
No modified residues

Experiments and Validation Details

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

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