Rpd3L complex

GO:0033698 · Other · Multiprotein complex · Proposed

A histone deacetylase complex which deacetylates histones preferentially in promoter regions. Composed of a two copies of catalytic histone deacetylase subunit (S. pombe Clr6/ S. cerevisiae Rpd3p), an Sds-3 family protein (S. pombe /S. cerevisiae Sds3(p) ), two copies of SIN3 family co-repressor (S. pombe Pst1/ S. cerevisiae Sin3p, a WD repeat protein/ histone chaperone (S. pombe Prw1/ S. cerevisiae Ume1p), and a zf- PHD finger ( S. pombe Png2/ S. cerevisiae Pho23p), plus 4 additional subunits, and associated factors. [GO:0033698]

Synonyms: Clr6 histone deacetylase complex I/I'; Clr6L complex; Rpd3C(L); Sin3L complex

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	Stoichiometry	Essential	Role
Rpd3 Rpd3L deacetylase subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	RPD3	2	UNKNOWN	Catalytic histone deacetylase constituent of the budding-yeast Rpd3L complex. `GO:0033698` GO and SGD annotate budding-yeast RPD3 as part of the Rpd3L complex under GO:0033698. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L and Rpd3S by MudPIT analysis in budding yeast.
Sin3 Rpd3L corepressor subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	SIN3	2	UNKNOWN	SIN3-family corepressor constituent of the budding-yeast Rpd3L complex. `GO:0033698` GO and SGD annotate budding-yeast SIN3 as part of the Rpd3L complex under GO:0033698. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L and Rpd3S by MudPIT analysis in budding yeast.
Ume1 Rpd3L WD-repeat subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	UME1		UNKNOWN	WD-repeat histone-chaperone constituent of the budding-yeast Rpd3L complex. `GO:0033698` GO and SGD annotate budding-yeast UME1 as part of the Rpd3L complex under GO:0033698. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L and Rpd3S by MudPIT analysis in budding yeast.
Sds3 Rpd3L subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	SDS3		UNKNOWN	Sds3-family constituent of the budding-yeast Rpd3L complex. `GO:0033698` GO and SGD annotate budding-yeast SDS3 as part of the Rpd3L complex under GO:0033698. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L and Rpd3S by MudPIT analysis in budding yeast.
Pho23 Rpd3L PHD-finger subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	PHO23		UNKNOWN	PHD-finger constituent of the budding-yeast Rpd3L complex. `GO:0033698` GO and SGD annotate budding-yeast PHO23 as part of the Rpd3L complex under GO:0033698. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L and Rpd3S by MudPIT analysis in budding yeast.
Sap30 Rpd3L subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	SAP30		UNKNOWN	Protein constituent of the budding-yeast Rpd3L complex. `GO:0033698` GO and SGD annotate budding-yeast SAP30 as part of the Rpd3L complex under GO:0033698. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L and Rpd3S by MudPIT analysis in budding yeast.
Dep1 Rpd3L subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	DEP1		UNKNOWN	Protein constituent of the budding-yeast Rpd3L complex. `GO:0033698` GO and SGD annotate budding-yeast DEP1 as part of the Rpd3L complex under GO:0033698. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L and Rpd3S by MudPIT analysis in budding yeast.
Cti6 Rpd3L subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	CTI6		UNKNOWN	Protein constituent of the budding-yeast Rpd3L complex. `GO:0033698` GO and SGD annotate budding-yeast CTI6 as part of the Rpd3L complex under GO:0033698. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L and Rpd3S by MudPIT analysis in budding yeast.
Rxt2 Rpd3L subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	RXT2		UNKNOWN	Protein constituent of the budding-yeast Rpd3L complex. `GO:0033698` GO and SGD annotate budding-yeast RXT2 as part of the Rpd3L complex under GO:0033698. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L and Rpd3S by MudPIT analysis in budding yeast.
Rxt3 Rpd3L subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	RXT3		UNKNOWN	Protein constituent of the budding-yeast Rpd3L complex. `GO:0033698` GO and SGD annotate budding-yeast RXT3 as part of the Rpd3L complex under GO:0033698. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L and Rpd3S by MudPIT analysis in budding yeast.
Ash1 Rpd3L subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	ASH1		UNKNOWN	Rpd3L-associated protein curated to the budding-yeast Rpd3L complex. `GO:0033698` GO and SGD annotate budding-yeast ASH1 as part of the Rpd3L complex under GO:0033698. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L and Rpd3S by MudPIT analysis in budding yeast.
Ume6 Rpd3L subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	UME6		UNKNOWN	Rpd3L-associated protein curated to the budding-yeast Rpd3L complex. `GO:0033698` GO and SGD annotate budding-yeast UME6 as part of the Rpd3L complex under GO:0033698. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L and Rpd3S by MudPIT analysis in budding yeast.

Taxonomic distribution

NCBITaxon:4932 Saccharomyces cerevisiae — COMMON: Budding yeast is the organism in which SGD annotates Rpd3L components to GO:0033698 with direct experimental evidence from the 2005 Rpd3L/Rpd3S Cell papers. [GO:0033698]

Canonical examples

NCBITaxon:4932 Saccharomyces cerevisiae — Carrozza et al. 2005 and Keogh et al. 2005 resolved the larger Rpd3C(L) histone deacetylase complex as distinct from the smaller Rpd3C(S) complex in budding yeast. [DOI:10.1016/j.cell.2005.10.025]

Functions

histone deacetylase activity GO:0004407 — The Rpd3L complex is an Rpd3-containing histone deacetylase complex that preferentially deacetylates histones in promoter regions.
- GO:0033698 GO:0033698 defines Rpd3L as a histone deacetylase complex that preferentially deacetylates histones in promoter 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 characterized Rpd3L as one of two budding-yeast Rpd3 histone deacetylase complexes.
- DOI:10.1016/j.cell.2005.10.025 Keogh et al. 2005 characterized Rpd3C(L) as the larger Rpd3 complex.

Mechanism graphs

Rpd3L carries yeast histone deacetylase activity (FUNCTION)

In Saccharomyces cerevisiae, the Rpd3L complex contains Rpd3p, Sin3p, Ume1p, Sds3p, Pho23p, Sap30p, Dep1p, Cti6p, Rxt2p, Rxt3p, Ash1p and Ume6p.

Subject	Predicate	Object	Evidence
Rpd3 Rpd3L deacetylase subunit	contributes to	Rpd3L complex	`GO:0033698` GO:0033698 defines the Rpd3L complex and SGD annotates this protein to it. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L by MudPIT analysis.
Sin3 Rpd3L corepressor subunit	contributes to	Rpd3L complex	`GO:0033698` GO:0033698 defines the Rpd3L complex and SGD annotates this protein to it. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L by MudPIT analysis.
Ume1 Rpd3L WD-repeat subunit	contributes to	Rpd3L complex	`GO:0033698` GO:0033698 defines the Rpd3L complex and SGD annotates this protein to it. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L by MudPIT analysis.
Sds3 Rpd3L subunit	contributes to	Rpd3L complex	`GO:0033698` GO:0033698 defines the Rpd3L complex and SGD annotates this protein to it. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L by MudPIT analysis.
Pho23 Rpd3L PHD-finger subunit	contributes to	Rpd3L complex	`GO:0033698` GO:0033698 defines the Rpd3L complex and SGD annotates this protein to it. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L by MudPIT analysis.
Sap30 Rpd3L subunit	contributes to	Rpd3L complex	`GO:0033698` GO:0033698 defines the Rpd3L complex and SGD annotates this protein to it. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L by MudPIT analysis.
Dep1 Rpd3L subunit	contributes to	Rpd3L complex	`GO:0033698` GO:0033698 defines the Rpd3L complex and SGD annotates this protein to it. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L by MudPIT analysis.
Cti6 Rpd3L subunit	contributes to	Rpd3L complex	`GO:0033698` GO:0033698 defines the Rpd3L complex and SGD annotates this protein to it. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L by MudPIT analysis.
Rxt2 Rpd3L subunit	contributes to	Rpd3L complex	`GO:0033698` GO:0033698 defines the Rpd3L complex and SGD annotates this protein to it. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L by MudPIT analysis.
Rxt3 Rpd3L subunit	contributes to	Rpd3L complex	`GO:0033698` GO:0033698 defines the Rpd3L complex and SGD annotates this protein to it. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L by MudPIT analysis.
Ash1 Rpd3L subunit	contributes to	Rpd3L complex	`GO:0033698` GO:0033698 defines the Rpd3L complex and SGD annotates this protein to it. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L by MudPIT analysis.
Ume6 Rpd3L subunit	contributes to	Rpd3L complex	`GO:0033698` GO:0033698 defines the Rpd3L complex and SGD annotates this protein to it. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L by MudPIT analysis.
Rpd3L complex	supports	histone deacetylase activity	`GO:0033698` GO:0033698 defines Rpd3L as a histone deacetylase complex. `GO:0004407` GO:0004407 is the molecular-function term for histone deacetylase activity. `DOI:10.1016/j.cell.2005.10.023` Carrozza et al. 2005 characterized Rpd3L as an Rpd3 histone deacetylase complex.

Discussions

CURATION_TODO (OPEN): Resolve exact source-neutral family groundings for the Rpd3L constituents. GO:0033698 plus direct SGD annotations define these budding-yeast proteins as Rpd3L complex constituents or associated Rpd3L factors. Exact cross-eukaryotic InterPro, Pfam, NCBIfam or UniProt family boundaries for these Rpd3L subunit classes need narrower curation before these component labels can be grounded.

Evidence

GO:0033698 Gene Ontology cellular-component term for the Rpd3L complex and its exact Clr6L, Rpd3C(L) and Sin3L 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.
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.
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

2026-09-27T04:02:24Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-09-27T04:03:15Z codex · EXPANDED_RECORD — Added GO exact synonyms, Sin3-type-complex parentage, chromatin/nuclear-chromosome parthood, twelve budding-yeast Rpd3L constituent rows, budding-yeast scope, histone deacetylase activity, GO/PubMed/DOI evidence, a nonmechanistic function graph, and an Rpd3L subunit-grounding TODO.

Source: data/structures/other/rpd3l_complex.yaml