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Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in close state

Source organisms:
Biochemical function: protein binding
Biological process: regulation of DNA-templated DNA replication initiation
Cellular component: nucleus

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EC 3.5.1.98: Histone deacetylase

Reaction catalysed:
Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone
Systematic name:
Histone amidohydrolase
Alternative Name(s):
  • HDAC

GO terms

Sequence families

Pfam Protein families (Pfam)
PF00125
Domain description: Core histone H2A/H2B/H3/H4
Occurring in:
  1. Histone H3.2
  2. Histone H2A type 1
  3. Histone H2B 1.1
The deposited structure of PDB entry 7yi4 contains 2 copies of Pfam domain PF00125 (Core histone H2A/H2B/H3/H4) in Histone H2A. Showing 1 copy in chain G [auth I].
The deposited structure of PDB entry 7yi4 contains 2 copies of Pfam domain PF00125 (Core histone H2A/H2B/H3/H4) in Histone H2B 1.1. Showing 1 copy in chain H [auth J].
The deposited structure of PDB entry 7yi4 contains 2 copies of Pfam domain PF00125 (Core histone H2A/H2B/H3/H4) in Histone H3. Showing 1 copy in chain O [auth G].

PF02671
Domain description: Paired amphipathic helix repeat
Occurring in:
  1. Transcriptional regulatory protein SIN3
The deposited structure of PDB entry 7yi4 contains 3 copies of Pfam domain PF02671 (Paired amphipathic helix repeat) in Transcriptional regulatory protein SIN3. Showing 3 copies in chain A (some of the copies are out of the observed residue ranges!).

PF16211
Domain description: C-terminus of histone H2A
Occurring in:
  1. Histone H2A type 1
The deposited structure of PDB entry 7yi4 contains 2 copies of Pfam domain PF16211 (C-terminus of histone H2A) in Histone H2A. Showing 1 copy in chain G [auth I].

PF15511
Domain description: Centromere kinetochore component CENP-T histone fold
Occurring in:
  1. Histone H4
The deposited structure of PDB entry 7yi4 contains 2 copies of Pfam domain PF15511 (Centromere kinetochore component CENP-T histone fold) in Histone H4. Showing 1 copy in chain I [auth L].

PF00628
Domain description: PHD-finger
Occurring in:
  1. Transcriptional regulatory protein RCO1
The deposited structure of PDB entry 7yi4 contains 2 copies of Pfam domain PF00628 (PHD-finger) in Transcriptional regulatory protein RCO1. Showing 1 copy in chain D.

PF05712
Domain description: MRG
Occurring in:
  1. Chromatin modification-related protein EAF3
The deposited structure of PDB entry 7yi4 contains 2 copies of Pfam domain PF05712 (MRG) in Chromatin modification-related protein EAF3. Showing 1 copy in chain C.

PF22732
Domain description: MSL3 chromodomain-like
Occurring in:
  1. Chromatin modification-related protein EAF3

PF11717
Domain description: RNA binding activity-knot of a chromodomain
Occurring in:
  1. Chromatin modification-related protein EAF3
The deposited structure of PDB entry 7yi4 contains 2 copies of Pfam domain PF11717 (RNA binding activity-knot of a chromodomain) in Chromatin modification-related protein EAF3. Showing 1 copy in chain C.

PF00850
Domain description: Histone deacetylase domain
Occurring in:
  1. Histone deacetylase RPD3
The deposited structure of PDB entry 7yi4 contains 1 copy of Pfam domain PF00850 (Histone deacetylase domain) in Histone deacetylase RPD3. Showing 1 copy in chain B.

PF16879
Domain description: C-terminal domain of Sin3a protein
Occurring in:
  1. Transcriptional regulatory protein SIN3
The deposited structure of PDB entry 7yi4 contains 1 copy of Pfam domain PF16879 (C-terminal domain of Sin3a protein) in Transcriptional regulatory protein SIN3. Showing 1 copy in chain A.

PF08295
Domain description: Sin3 family co-repressor
Occurring in:
  1. Transcriptional regulatory protein SIN3
The deposited structure of PDB entry 7yi4 contains 1 copy of Pfam domain PF08295 (Sin3 family co-repressor) in Transcriptional regulatory protein SIN3. Showing 1 copy in chain A.

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