Set3 complex

GO:0034967 · Other · Multiprotein complex · Proposed

A histone deacetylase complex that is involved in transcriptional regulation. In S. cerevisiae, this complex consists of Set3p, Snt1p, Hos4p, Sif2p, Cpr1p, Hos2p, and Hst1p. [GO:0034967]

Synonyms: HDAC3 complex; SET3C

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
Set3 SET3C subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	SET3	UNKNOWN	SET/PHD-domain constituent that gives the budding-yeast Set3 histone deacetylase complex its name. `GO:0034967` GO:0034967 defines the S. cerevisiae Set3 complex as containing Set3p. `DOI:10.1101/gad.207401` Pijnappel et al. 2001 identified Set3p as a constituent of budding-yeast Set3C.
Snt1 SET3C subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	SNT1	UNKNOWN	Protein constituent of the budding-yeast Set3 histone deacetylase complex. `GO:0034967` GO:0034967 defines the S. cerevisiae Set3 complex as containing Snt1p. `DOI:10.1101/gad.207401` Pijnappel et al. 2001 identified Snt1p as a constituent of budding-yeast Set3C.
Hos4 SET3C subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	HOS4	UNKNOWN	Protein constituent of the budding-yeast Set3 histone deacetylase complex, corresponding to the YIL112w protein identified with Set3C. `GO:0034967` GO:0034967 defines the S. cerevisiae Set3 complex as containing Hos4p. `DOI:10.1101/gad.207401` Pijnappel et al. 2001 identified YIL112w as a constituent of budding-yeast Set3C; GO:0034967 curates that subunit with the Hos4p name.
Sif2 SET3C subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	SIF2	UNKNOWN	Protein constituent of the budding-yeast Set3 histone deacetylase complex. `GO:0034967` GO:0034967 defines the S. cerevisiae Set3 complex as containing Sif2p. `DOI:10.1101/gad.207401` Pijnappel et al. 2001 identified Sif2p as a constituent of budding-yeast Set3C.
Cpr1 SET3C subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	CPR1	UNKNOWN	Cyclophilin constituent of the budding-yeast Set3 histone deacetylase complex. `GO:0034967` GO:0034967 defines the S. cerevisiae Set3 complex as containing Cpr1p. `DOI:10.1101/gad.207401` Pijnappel et al. 2001 identified Cpr1p as a constituent of budding-yeast Set3C.
Hos2 SET3C deacetylase subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	HOS2	UNKNOWN	Putative histone deacetylase constituent of the budding-yeast Set3 complex. `GO:0034967` GO:0034967 defines the S. cerevisiae Set3 complex as containing Hos2p. `DOI:10.1101/gad.207401` Pijnappel et al. 2001 identified Hos2p as a constituent of budding-yeast Set3C.
Hst1 SET3C deacetylase subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	HST1	UNKNOWN	NAD-dependent putative histone deacetylase constituent of the budding-yeast Set3 complex. `GO:0034967` GO:0034967 defines the S. cerevisiae Set3 complex as containing Hst1p. `DOI:10.1101/gad.207401` Pijnappel et al. 2001 identified Hst1p as a constituent of budding-yeast Set3C.

Taxonomic distribution

NCBITaxon:4932 Saccharomyces cerevisiae — COMMON: Budding yeast is the organism in which GO:0034967 defines the Set3 complex as a seven-subunit histone deacetylase complex. [GO:0034967]

Canonical examples

NCBITaxon:4932 Saccharomyces cerevisiae — Pijnappel et al. 2001 identified Set3C as a budding-yeast complex containing Set3, Snt1, YIL112w/Hos4, Sif2, Cpr1, Hos2 and Hst1. [DOI:10.1101/gad.207401]

Functions

histone deacetylase activity GO:0004407 — The Set3 complex is a histone deacetylase complex that contains the Hos2 and Hst1 deacetylase constituents.
- GO:0034967 GO:0034967 defines the Set3 complex as a histone deacetylase complex involved in transcriptional regulation.
- GO:0004407 GO:0004407 is the Gene Ontology molecular-function term for histone deacetylase activity.
- DOI:10.1101/gad.207401 Pijnappel et al. 2001 found NAD-dependent and NAD-independent deacetylase activities in Set3C in vitro.

Mechanism graphs

Set3C carries yeast histone deacetylase activity (FUNCTION)

In Saccharomyces cerevisiae, Set3p, Snt1p, Hos4p, Sif2p, Cpr1p, Hos2p and Hst1p form the Set3C histone deacetylase complex.

Subject	Predicate	Object	Evidence
Set3 SET3C subunit	contributes to	Set3 complex	`GO:0034967` GO:0034967 defines Set3p as a Set3 complex constituent.
Snt1 SET3C subunit	contributes to	Set3 complex	`GO:0034967` GO:0034967 defines Snt1p as a Set3 complex constituent.
Hos4 SET3C subunit	contributes to	Set3 complex	`GO:0034967` GO:0034967 defines Hos4p as a Set3 complex constituent.
Sif2 SET3C subunit	contributes to	Set3 complex	`GO:0034967` GO:0034967 defines Sif2p as a Set3 complex constituent.
Cpr1 SET3C subunit	contributes to	Set3 complex	`GO:0034967` GO:0034967 defines Cpr1p as a Set3 complex constituent.
Hos2 SET3C deacetylase subunit	contributes to	Set3 complex	`GO:0034967` GO:0034967 defines Hos2p as a Set3 complex constituent.
Hst1 SET3C deacetylase subunit	contributes to	Set3 complex	`GO:0034967` GO:0034967 defines Hst1p as a Set3 complex constituent.
Set3 complex	supports	histone deacetylase activity	`GO:0034967` GO:0034967 defines the Set3 complex as a histone deacetylase complex. `GO:0004407` GO:0004407 is the molecular-function term for histone deacetylase activity. `DOI:10.1101/gad.207401` Pijnappel et al. 2001 found in vitro NAD-dependent and NAD-independent deacetylase activities in Set3C.

Discussions

CURATION_TODO (OPEN): Resolve exact source-neutral family groundings for the Set3C constituents. GO:0034967 defines the budding-yeast Set3p, Snt1p, Hos4p, Sif2p, Cpr1p, Hos2p and Hst1p proteins as Set3 complex constituents. Exact cross-eukaryotic InterPro, Pfam, NCBIfam or UniProt family boundaries for these Set3C subunit classes need narrower curation before these component labels can be grounded.

Evidence

GO:0034967 Gene Ontology cellular-component term for the Set3 complex and its exact HDAC3 complex and SET3C synonyms.
GO:0000118 Gene Ontology cellular-component parent term for histone deacetylase complexes.
GO:0000228 Gene Ontology cellular-component term for nuclear chromosome.
GO:0000785 — chromatin Gene Ontology cellular-component term for chromatin.
GO:0004407 Gene Ontology molecular-function term for histone deacetylase activity.
PMID:11711434 PubMed identifier for Pijnappel et al. 2001, the Set3C Genes and Development paper cited by GO:0034967.
DOI:10.1101/gad.207401 DOI for Pijnappel et al. 2001, 'The S. cerevisiae SET3 complex includes two histone deacetylases, Hos2 and Hst1, and is a meiotic-specific repressor of the sporulation gene program', verified through NCBI E-utilities.

Curation history

2026-09-26T03:40:05Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-09-26T03:40:52Z codex · EXPANDED_RECORD — Added Set3 exact synonymy, histone-deacetylase-complex parentage, chromatin/nuclear-chromosome parthood, Set3C constituent rows, budding-yeast scope, histone deacetylase activity, GO/PubMed/DOI evidence, a nonmechanistic function graph, and a Set3C subunit-grounding TODO.
2026-09-26T03:43:21Z codex · FIX_HOS4_PRIOR_NAME — Clarified that the Set3C primary paper identified the GO-curated Hos4p subunit under its YIL112w name.

Source: data/structures/other/set3_complex.yaml