Rpd3L-Expanded complex

GO:0070210 · Other · Multiprotein complex · Proposed

A protein complex that contains a histone deacetylase and is part of the chromatin remodeling machinery. In Saccharomyces cerevisiae this complex contains the Rpd3p, Sin3p, Ume1p, Pho23p, Sap30p, Sds3p, Cti6p, Rxt2p, Rxt3p, Dep1p, Ume6p, Ash1p, Dot6p, Snt1, Sif2p, Set3p, Hos2p, Tos4p and Tod6p proteins. [GO:0070210]

Synonyms: Clr6-LE complex; Rpd3-LE

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 Rpd3L-Expanded deacetylase subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	RPD3	UNKNOWN	Histone deacetylase constituent of the budding-yeast Rpd3L-Expanded complex. `GO:0070210` GO:0070210 defines the S. cerevisiae Rpd3L-Expanded complex as containing Rpd3p.
Sin3 Rpd3L-Expanded subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	SIN3	UNKNOWN	Protein constituent of the budding-yeast Rpd3L-Expanded histone deacetylase complex. `GO:0070210` GO:0070210 defines the S. cerevisiae Rpd3L-Expanded complex as containing Sin3p.
Ume1 Rpd3L-Expanded subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	UME1	UNKNOWN	Protein constituent of the budding-yeast Rpd3L-Expanded histone deacetylase complex. `GO:0070210` GO:0070210 defines the S. cerevisiae Rpd3L-Expanded complex as containing Ume1p.
Pho23 Rpd3L-Expanded subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	PHO23	UNKNOWN	Protein constituent of the budding-yeast Rpd3L-Expanded histone deacetylase complex. `GO:0070210` GO:0070210 defines the S. cerevisiae Rpd3L-Expanded complex as containing Pho23p.
Sap30 Rpd3L-Expanded subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	SAP30	UNKNOWN	Protein constituent of the budding-yeast Rpd3L-Expanded histone deacetylase complex. `GO:0070210` GO:0070210 defines the S. cerevisiae Rpd3L-Expanded complex as containing Sap30p.
Sds3 Rpd3L-Expanded subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	SDS3	UNKNOWN	Protein constituent of the budding-yeast Rpd3L-Expanded histone deacetylase complex. `GO:0070210` GO:0070210 defines the S. cerevisiae Rpd3L-Expanded complex as containing Sds3p.
Cti6 Rpd3L-Expanded subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	CTI6	UNKNOWN	Protein constituent of the budding-yeast Rpd3L-Expanded histone deacetylase complex. `GO:0070210` GO:0070210 defines the S. cerevisiae Rpd3L-Expanded complex as containing Cti6p.
Rxt2 Rpd3L-Expanded subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	RXT2	UNKNOWN	Protein constituent of the budding-yeast Rpd3L-Expanded histone deacetylase complex. `GO:0070210` GO:0070210 defines the S. cerevisiae Rpd3L-Expanded complex as containing Rxt2p.
Rxt3 Rpd3L-Expanded subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	RXT3	UNKNOWN	Protein constituent of the budding-yeast Rpd3L-Expanded histone deacetylase complex. `GO:0070210` GO:0070210 defines the S. cerevisiae Rpd3L-Expanded complex as containing Rxt3p.
Dep1 Rpd3L-Expanded subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	DEP1	UNKNOWN	Protein constituent of the budding-yeast Rpd3L-Expanded histone deacetylase complex. `GO:0070210` GO:0070210 defines the S. cerevisiae Rpd3L-Expanded complex as containing Dep1p.
Ume6 Rpd3L-Expanded subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	UME6	UNKNOWN	Protein constituent of the budding-yeast Rpd3L-Expanded histone deacetylase complex. `GO:0070210` GO:0070210 defines the S. cerevisiae Rpd3L-Expanded complex as containing Ume6p.
Ash1 Rpd3L-Expanded subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	ASH1	UNKNOWN	Protein constituent of the budding-yeast Rpd3L-Expanded histone deacetylase complex. `GO:0070210` GO:0070210 defines the S. cerevisiae Rpd3L-Expanded complex as containing Ash1p.
Dot6 Rpd3L-Expanded subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	DOT6	UNKNOWN	Protein constituent of the budding-yeast Rpd3L-Expanded histone deacetylase complex. `GO:0070210` GO:0070210 defines the S. cerevisiae Rpd3L-Expanded complex as containing Dot6p.
Snt1 Rpd3L-Expanded subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	SNT1	UNKNOWN	Protein constituent of the budding-yeast Rpd3L-Expanded histone deacetylase complex. `GO:0070210` GO:0070210 defines the S. cerevisiae Rpd3L-Expanded complex as containing Snt1p.
Sif2 Rpd3L-Expanded subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	SIF2	UNKNOWN	Protein constituent of the budding-yeast Rpd3L-Expanded histone deacetylase complex. `GO:0070210` GO:0070210 defines the S. cerevisiae Rpd3L-Expanded complex as containing Sif2p.
Set3 Rpd3L-Expanded subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	SET3	UNKNOWN	Protein constituent of the budding-yeast Rpd3L-Expanded histone deacetylase complex. `GO:0070210` GO:0070210 defines the S. cerevisiae Rpd3L-Expanded complex as containing Set3p.
Hos2 Rpd3L-Expanded subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	HOS2	UNKNOWN	Protein constituent of the budding-yeast Rpd3L-Expanded histone deacetylase complex. `GO:0070210` GO:0070210 defines the S. cerevisiae Rpd3L-Expanded complex as containing Hos2p.
Tos4 Rpd3L-Expanded subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	TOS4	UNKNOWN	Protein constituent of the budding-yeast Rpd3L-Expanded histone deacetylase complex. `GO:0070210` GO:0070210 defines the S. cerevisiae Rpd3L-Expanded complex as containing Tos4p.
Tod6 Rpd3L-Expanded subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	TOD6	UNKNOWN	Protein constituent of the budding-yeast Rpd3L-Expanded histone deacetylase complex. `GO:0070210` GO:0070210 defines the S. cerevisiae Rpd3L-Expanded complex as containing Tod6p.

Taxonomic distribution

NCBITaxon:4932 Saccharomyces cerevisiae — COMMON: Budding yeast is the organism in which GO:0070210 defines the Rpd3L-Expanded complex as a Rpd3-containing extension of the Rpd3L complex. [GO:0070210]

Canonical examples

NCBITaxon:4932 Saccharomyces cerevisiae — Shevchenko et al. 2008 identified Rpd3-LE as an Rpd3-containing complex in budding-yeast Chromatin Central and assigned it as an extension of the Rpd3L complex that includes the Set3 complex core. [DOI:10.1186/gb-2008-9-11-r167]

Functions

histone deacetylase activity GO:0004407 — The Rpd3L-Expanded complex is an Rpd3-containing histone deacetylase complex.
- GO:0070210 GO:0070210 defines Rpd3L-Expanded as a histone-deacetylase-containing complex.
- GO:0004407 GO:0004407 is the Gene Ontology molecular-function term for histone deacetylase activity.
- DOI:10.1186/gb-2008-9-11-r167 Shevchenko et al. 2008 assigned Rpd3-LE as one of two new Rpd3-containing complexes in budding-yeast Chromatin Central.

Mechanism graphs

Rpd3L-Expanded carries yeast histone deacetylase activity (FUNCTION)

In Saccharomyces cerevisiae, the Rpd3L-Expanded complex contains Rpd3p, Sin3p, Ume1p, Pho23p, Sap30p, Sds3p, Cti6p, Rxt2p, Rxt3p, Dep1p, Ume6p, Ash1p, Dot6p, Snt1, Sif2p, Set3p, Hos2p, Tos4p and Tod6p.

Subject	Predicate	Object	Evidence
Rpd3 Rpd3L-Expanded deacetylase subunit	contributes to	Rpd3L-Expanded complex	`GO:0070210` GO:0070210 defines Rpd3p as an Rpd3L-Expanded complex constituent.
Sin3 Rpd3L-Expanded subunit	contributes to	Rpd3L-Expanded complex	`GO:0070210` GO:0070210 defines Sin3p as an Rpd3L-Expanded complex constituent.
Ume1 Rpd3L-Expanded subunit	contributes to	Rpd3L-Expanded complex	`GO:0070210` GO:0070210 defines Ume1p as an Rpd3L-Expanded complex constituent.
Pho23 Rpd3L-Expanded subunit	contributes to	Rpd3L-Expanded complex	`GO:0070210` GO:0070210 defines Pho23p as an Rpd3L-Expanded complex constituent.
Sap30 Rpd3L-Expanded subunit	contributes to	Rpd3L-Expanded complex	`GO:0070210` GO:0070210 defines Sap30p as an Rpd3L-Expanded complex constituent.
Sds3 Rpd3L-Expanded subunit	contributes to	Rpd3L-Expanded complex	`GO:0070210` GO:0070210 defines Sds3p as an Rpd3L-Expanded complex constituent.
Cti6 Rpd3L-Expanded subunit	contributes to	Rpd3L-Expanded complex	`GO:0070210` GO:0070210 defines Cti6p as an Rpd3L-Expanded complex constituent.
Rxt2 Rpd3L-Expanded subunit	contributes to	Rpd3L-Expanded complex	`GO:0070210` GO:0070210 defines Rxt2p as an Rpd3L-Expanded complex constituent.
Rxt3 Rpd3L-Expanded subunit	contributes to	Rpd3L-Expanded complex	`GO:0070210` GO:0070210 defines Rxt3p as an Rpd3L-Expanded complex constituent.
Dep1 Rpd3L-Expanded subunit	contributes to	Rpd3L-Expanded complex	`GO:0070210` GO:0070210 defines Dep1p as an Rpd3L-Expanded complex constituent.
Ume6 Rpd3L-Expanded subunit	contributes to	Rpd3L-Expanded complex	`GO:0070210` GO:0070210 defines Ume6p as an Rpd3L-Expanded complex constituent.
Ash1 Rpd3L-Expanded subunit	contributes to	Rpd3L-Expanded complex	`GO:0070210` GO:0070210 defines Ash1p as an Rpd3L-Expanded complex constituent.
Dot6 Rpd3L-Expanded subunit	contributes to	Rpd3L-Expanded complex	`GO:0070210` GO:0070210 defines Dot6p as an Rpd3L-Expanded complex constituent.
Snt1 Rpd3L-Expanded subunit	contributes to	Rpd3L-Expanded complex	`GO:0070210` GO:0070210 defines Snt1p as an Rpd3L-Expanded complex constituent.
Sif2 Rpd3L-Expanded subunit	contributes to	Rpd3L-Expanded complex	`GO:0070210` GO:0070210 defines Sif2p as an Rpd3L-Expanded complex constituent.
Set3 Rpd3L-Expanded subunit	contributes to	Rpd3L-Expanded complex	`GO:0070210` GO:0070210 defines Set3p as an Rpd3L-Expanded complex constituent.
Hos2 Rpd3L-Expanded subunit	contributes to	Rpd3L-Expanded complex	`GO:0070210` GO:0070210 defines Hos2p as an Rpd3L-Expanded complex constituent.
Tos4 Rpd3L-Expanded subunit	contributes to	Rpd3L-Expanded complex	`GO:0070210` GO:0070210 defines Tos4p as an Rpd3L-Expanded complex constituent.
Tod6 Rpd3L-Expanded subunit	contributes to	Rpd3L-Expanded complex	`GO:0070210` GO:0070210 defines Tod6p as an Rpd3L-Expanded complex constituent.
Rpd3L-Expanded complex	supports	histone deacetylase activity	`GO:0070210` GO:0070210 defines Rpd3L-Expanded as a histone-deacetylase-containing complex. `GO:0004407` GO:0004407 is the molecular-function term for histone deacetylase activity.

Discussions

CURATION_TODO (OPEN): Resolve exact source-neutral family groundings for the Rpd3L-Expanded constituents. GO:0070210 defines 19 budding-yeast proteins as Rpd3L-Expanded complex constituents. Exact cross-eukaryotic InterPro, Pfam, NCBIfam or UniProt family boundaries for these Rpd3L-Expanded subunit classes need narrower curation before these component labels can be grounded.

Evidence

GO:0070210 Gene Ontology cellular-component term for the Rpd3L-Expanded complex and its exact Clr6-LE synonym.
GO:0000118 Gene Ontology cellular-component parent term for 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:19040720 PubMed identifier for Shevchenko et al. 2008, the Genome Biology Chromatin Central paper cited by GO:0070210.
DOI:10.1186/gb-2008-9-11-r167 DOI for Shevchenko et al. 2008, 'Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment', verified through NCBI E-utilities.

Curation history

2026-09-26T04:32:15Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-09-26T04:32:57Z codex · EXPANDED_RECORD — Added Rpd3-LE/Clr6-LE exact synonymy, histone-deacetylase-complex parentage, chromatin/nuclear-chromosome parthood, nineteen Rpd3L-Expanded constituent rows, budding-yeast scope, histone deacetylase activity, GO/PubMed/DOI evidence, a nonmechanistic function graph, and a Rpd3L-Expanded subunit-grounding TODO.

Source: data/structures/other/rpd3l_expanded_complex.yaml