› › Structure analysis

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

Electron Microscopy
3.9Å resolution
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:
Assembly composition:
hetero octadecamer (preferred)
Entry contents: 9 distinct polypeptide molecules
2 distinct DNA molecules

Quick links

Assemblies

Assembly 1 (preferred)
Download    3D Visualisation
Multimeric state: hetero octadecamer
Accessible surface area: 165736.82 Å2
Buried surface area: 89376.83 Å2
Dissociation area: 806.52 Å2
Dissociation energy (ΔGdiss): -18.89 kcal/mol
Dissociation entropy (TΔSdiss): 28.51 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-244359

Macromolecules

Transcriptional regulatory protein SIN3
Chain: A
Length: 1536 amino acids
Theoretical weight: 175.05 KDa
Source organism: Saccharomyces cerevisiae
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 8w9d, assembly 1, front view.
Transcriptional regulatory protein SIN3 in PDB entry 8w9d, assembly 1, side view.
Transcriptional regulatory protein SIN3 in PDB entry 8w9d, assembly 1, top view.
Molecule details ›

Search similar proteins

Transcriptional regulatory protein RCO1
Chains: E, F
Length: 684 amino acids
Theoretical weight: 78.95 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q04779 (Residues: 1-684; Coverage: 100%)
Gene names: RCO1, YM9916.14, YMR075W
Pfam: PHD-finger
Transcriptional regulatory protein RCO1 in PDB entry 8w9d, assembly 1, front view.
Transcriptional regulatory protein RCO1 in PDB entry 8w9d, assembly 1, side view.
Transcriptional regulatory protein RCO1 in PDB entry 8w9d, assembly 1, top view.
Molecule details ›

Search similar proteins

Histone deacetylase RPD3
Chain: B
Length: 433 amino acids
Theoretical weight: 48.96 KDa
Source organism: Saccharomyces cerevisiae
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 8w9d, assembly 1, front view.
Histone deacetylase RPD3 in PDB entry 8w9d, assembly 1, side view.
Histone deacetylase RPD3 in PDB entry 8w9d, assembly 1, top view.
Molecule details ›

Search similar proteins

Chromatin modification-related protein EAF3
Chains: C, D, G
Length: 401 amino acids
Theoretical weight: 45.27 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12432 (Residues: 1-401; Coverage: 100%)
Gene names: EAF3, YP9367.03C, YPR023C
Pfam:
Chromatin modification-related protein EAF3 in PDB entry 8w9d, assembly 1, front view.
Chromatin modification-related protein EAF3 in PDB entry 8w9d, assembly 1, side view.
Chromatin modification-related protein EAF3 in PDB entry 8w9d, assembly 1, top view.
Molecule details ›

Search similar proteins

Histone H3.1
Chains: a, e
Length: 136 amino acids
Theoretical weight: 15.44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P68431 (Residues: 1-136; Coverage: 100%)
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
Pfam: Core histone H2A/H2B/H3/H4
Histone H3.1 in PDB entry 8w9d, assembly 1, front view.
Histone H3.1 in PDB entry 8w9d, assembly 1, side view.
Histone H3.1 in PDB entry 8w9d, assembly 1, top view.
Molecule details ›

Search similar proteins

Histone H4
Chains: b, f
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62805 (Residues: 1-103; Coverage: 100%)
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
Pfam: Centromere kinetochore component CENP-T histone fold
Histone H4 in PDB entry 8w9d, assembly 1, front view.
Histone H4 in PDB entry 8w9d, assembly 1, side view.
Histone H4 in PDB entry 8w9d, assembly 1, top view.
Molecule details ›

Search similar proteins

Histone H2A type 1-B/E
Chains: c, g
Length: 130 amino acids
Theoretical weight: 14.17 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P04908 (Residues: 1-130; Coverage: 100%)
Gene names: H2AC4, H2AC8, H2AFA, H2AFM, HIST1H2AB, HIST1H2AE
Pfam:
Histone H2A type 1-B/E in PDB entry 8w9d, assembly 1, front view.
Histone H2A type 1-B/E in PDB entry 8w9d, assembly 1, side view.
Histone H2A type 1-B/E in PDB entry 8w9d, assembly 1, top view.
Molecule details ›

Search similar proteins

Histone H2B type 1-K
Chains: d, h
Length: 126 amino acids
Theoretical weight: 13.92 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O60814 (Residues: 1-126; Coverage: 100%)
Gene names: H2BC12, H2BFT, HIRIP1, HIST1H2BK
Pfam: Core histone H2A/H2B/H3/H4
Histone H2B type 1-K in PDB entry 8w9d, assembly 1, front view.
Histone H2B type 1-K in PDB entry 8w9d, assembly 1, side view.
Histone H2B type 1-K in PDB entry 8w9d, assembly 1, top view.
Molecule details ›

Search similar proteins

Unclear peptide
Chain: H
Length: 5 amino acids
Theoretical weight: 488 Da
Source organism: Saccharomyces cerevisiae
Unclear peptide in PDB entry 8w9d, assembly 1, front view.
Unclear peptide in PDB entry 8w9d, assembly 1, side view.
Unclear peptide in PDB entry 8w9d, assembly 1, top view.
Molecule details ›

Search similar proteins

DNA chain i
Name: 5-DNA
Representative chains: i
Length: 147 nucleotides
Theoretical weight: 45.37 KDa
5-DNA in PDB entry 8w9d, assembly 1, front view.
5-DNA in PDB entry 8w9d, assembly 1, side view.
5-DNA in PDB entry 8w9d, assembly 1, top view.
Molecule details ›

Search similar DNA

DNA chain j
Name: 3-DNA
Representative chains: j
Length: 147 nucleotides
Theoretical weight: 45.36 KDa
3-DNA in PDB entry 8w9d, assembly 1, front view.
3-DNA in PDB entry 8w9d, assembly 1, side view.
3-DNA in PDB entry 8w9d, assembly 1, top view.
Molecule details ›

Search similar DNA

Quick links