Rpd3S complex

GO:0032221 · Other · Multiprotein complex · Proposed

A eukaryotically conserved histone deacetylase complex which deacetylates histones across gene coding regions. Composed of a catalytic histone deacetylase subunit, a chromodomain protein, a SIN3 family co-repressor, and a WD repeat protein (Clr6p, Alp13p, Pst2p, and Prw1p respectively in Schizosaccharomyces; Rpd3p, Sin3p, Ume1p, Rco1p and Eaf3 in Saccharomyces; homologs thereof in other species). [GO:0032221]

Synonyms: Clr6-CII complex; Clr6 histone deacetylase complex II; Clr6 histone deacetylase complex II'; Clr6S complex; Rpd3C(S); Rpd3S; Sin3S

Part of: nuclear chromosome (GO:0000228); GO:0000785 — chromatin (no local record)

UniProt location names: UniProt Consortium, CC BY 4.0. Reference label and route sources.

Components

Component	Type	Part of / acts on	Grounding	Genes	Essential	Role
Rpd3 Rpd3S deacetylase subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	RPD3	UNKNOWN	Catalytic histone deacetylase constituent of the budding-yeast Rpd3S complex. `GO:0032221` GO:0032221 defines the Saccharomyces Rpd3S complex as containing Rpd3p. `DOI:10.1016/j.cell.2005.10.025` Keogh et al. 2005 characterized Rpd3C(S) as one of two distinct budding-yeast Rpd3 complexes.
Sin3 Rpd3S corepressor subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	SIN3	UNKNOWN	SIN3-family corepressor constituent shared by the budding-yeast Rpd3S and Rpd3L complexes. `GO:0032221` GO:0032221 defines the Saccharomyces Rpd3S complex as containing Sin3p. `DOI:10.1016/j.cell.2005.10.025` Keogh et al. 2005 reported that Rpd3C(S) shares Sin3 with the larger Rpd3C(L) complex.
Ume1 Rpd3S WD-repeat subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	UME1	UNKNOWN	WD-repeat constituent shared by the budding-yeast Rpd3S and Rpd3L complexes. `GO:0032221` GO:0032221 defines the Saccharomyces Rpd3S complex as containing Ume1p. `DOI:10.1016/j.cell.2005.10.025` Keogh et al. 2005 reported that Rpd3C(S) shares Ume1 with the larger Rpd3C(L) complex.
Rco1 Rpd3S subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	RCO1	UNKNOWN	Rpd3S-specific constituent of the budding-yeast complex. `GO:0032221` GO:0032221 defines the Saccharomyces Rpd3S complex as containing Rco1p. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 identified Rco1 as a subunit specific to budding-yeast Rpd3S. `DOI:10.1016/j.cell.2005.10.025` Keogh et al. 2005 identified Rco1 as a unique Rpd3C(S) subunit.
Eaf3 Rpd3S chromodomain subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	EAF3	UNKNOWN	Rpd3S-specific chromodomain constituent involved in methylated-nucleosome recruitment. `GO:0032221` GO:0032221 defines the Saccharomyces Rpd3S complex as containing Eaf3. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 identified Eaf3 as a subunit specific to budding-yeast Rpd3S. `DOI:10.1016/j.cell.2005.10.025` Keogh et al. 2005 identified Eaf3 as a unique Rpd3C(S) subunit and linked its chromodomain to recruitment to methylated nucleosomes.

Taxonomic distribution

NCBITaxon:4932 Saccharomyces cerevisiae — COMMON: Budding yeast is the organism in which GO:0032221 defines the Rpd3S complex as containing Rpd3p, Sin3p, Ume1p, Rco1p and Eaf3. [GO:0032221]

Canonical examples

NCBITaxon:4932 Saccharomyces cerevisiae — Keogh et al. 2005 and Carrozza et al. 2005 characterized Rpd3S/Rpd3C(S) as a budding-yeast Rpd3 histone deacetylase complex containing Rco1 and Eaf3 as smaller-complex-specific subunits. [DOI:10.1016/j.cell.2005.10.025]

Functions

histone deacetylase activity GO:0004407 — The Rpd3S complex deacetylates histones across gene coding regions through its Rpd3 catalytic subunit.
- GO:0032221 GO:0032221 defines Rpd3S as a histone deacetylase complex that deacetylates histones across gene coding regions.
- GO:0004407 GO:0004407 is the Gene Ontology molecular-function term for histone deacetylase activity.
- DOI:10.1016/j.cell.2005.10.023 Carrozza et al. 2005 found that RCO1 and EAF3 mutants disrupted open-reading-frame deacetylation and suppression of intragenic transcription.
- DOI:10.1016/j.cell.2005.10.025 Keogh et al. 2005 found that Eaf3 recruits Rpd3C(S) to Set2-methylated H3K36 nucleosomes for deacetylation of transcribed regions.

Mechanism graphs

Rpd3S carries yeast histone deacetylase activity (FUNCTION)

In Saccharomyces cerevisiae, Rpd3p, Sin3p, Ume1p, Rco1p and Eaf3 form the Rpd3S histone deacetylase complex.

Subject	Predicate	Object	Evidence
Rpd3 Rpd3S deacetylase subunit	contributes to	Rpd3S complex	`GO:0032221` GO:0032221 defines Rpd3p as an Rpd3S complex constituent. `DOI:10.1016/j.cell.2005.10.025` Keogh et al. 2005 characterized Rpd3C(S) as a Rpd3 histone deacetylase complex.
Sin3 Rpd3S corepressor subunit	contributes to	Rpd3S complex	`GO:0032221` GO:0032221 defines Sin3p as an Rpd3S complex constituent. `DOI:10.1016/j.cell.2005.10.025` Keogh et al. 2005 identified Sin3 as shared by Rpd3C(S) and Rpd3C(L).
Ume1 Rpd3S WD-repeat subunit	contributes to	Rpd3S complex	`GO:0032221` GO:0032221 defines Ume1p as an Rpd3S complex constituent. `DOI:10.1016/j.cell.2005.10.025` Keogh et al. 2005 identified Ume1 as shared by Rpd3C(S) and Rpd3C(L).
Rco1 Rpd3S subunit	contributes to	Rpd3S complex	`GO:0032221` GO:0032221 defines Rco1p as an Rpd3S complex constituent. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 identified Rco1 as an Rpd3S-specific subunit.
Eaf3 Rpd3S chromodomain subunit	contributes to	Rpd3S complex	`GO:0032221` GO:0032221 defines Eaf3 as an Rpd3S complex constituent. `DOI:10.1016/j.cell.2005.10.025` Keogh et al. 2005 identified Eaf3 as a unique Rpd3C(S) subunit.
Rpd3S complex	supports	histone deacetylase activity	`GO:0032221` GO:0032221 defines Rpd3S as a histone deacetylase complex. `GO:0004407` GO:0004407 is the molecular-function term for histone deacetylase activity. `DOI:10.1016/j.cell.2005.10.025` Keogh et al. 2005 linked Rpd3C(S) to deacetylation of transcribed regions.

Discussions

CURATION_TODO (OPEN): Resolve exact source-neutral family groundings for the Rpd3S constituents. GO:0032221 defines five budding-yeast proteins as Rpd3S complex constituents. Exact cross-eukaryotic InterPro, Pfam, NCBIfam or UniProt family boundaries for these Rpd3S subunit classes need narrower curation before these component labels can be grounded.

Evidence

GO:0032221 Gene Ontology cellular-component term for the Rpd3S complex and its exact Clr6-CII, Clr6S, Rpd3C(S), Rpd3S and Sin3S synonyms.
GO:0070822 Gene Ontology cellular-component parent term for Sin3-type histone deacetylase complexes.
GO:0000228 Gene Ontology cellular-component term for the nuclear chromosome.
GO:0000785 — chromatin Gene Ontology cellular-component term for chromatin.
GO:0004407 Gene Ontology molecular-function term for histone deacetylase activity.
PMID:16286007 PubMed identifier for Carrozza et al. 2005, the Cell Rpd3S coding-region deacetylation paper.
DOI:10.1016/j.cell.2005.10.023 DOI for Carrozza et al. 2005, 'Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription', verified through NCBI E-utilities.
PMID:16286008 PubMed identifier for Keogh et al. 2005, the Cell Rpd3C(S) H3K36me recruitment paper.
DOI:10.1016/j.cell.2005.10.025 DOI for Keogh et al. 2005, 'Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex', verified through NCBI E-utilities.

Curation history

2026-09-27T03:40:13Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-09-27T03:41:28Z codex · EXPANDED_RECORD — Added GO exact synonyms, Sin3-type-complex parentage, chromatin/nuclear-chromosome parthood, five budding-yeast Rpd3S constituent rows, budding-yeast scope, histone deacetylase activity, GO/PubMed/DOI evidence, a nonmechanistic function graph, and an Rpd3S subunit-grounding TODO.

Source: data/structures/other/rpd3s_complex.yaml