ArticleNature communications2023
Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 14 citations in OpenAlex.
- Alterations to the yeast chromatin landscape during hypoxia.bioRxiv : the preprint server for biology · 2026Article
- Cross-species R-DeeP profiling reveals a conserved core of RNA-dependent proteins in yeast.Nucleic acids research · 2026Article
- Rpd3L regulates transcription-replication conflict via H3K4 methylation-dependent and -independent chromatin mechanisms.Science advances · 2026Article
- Chromatin context-dependent deacetylation by the asymmetric Rpd3L.Nucleic acids research · 2026Article
- A de novo missense variant in MIDEAS results in increased deacetylase activity of the MiDAC HDAC complex causing a neurodevelopmental syndrome.Nature communications · 2025Article
- Mutations on the surface of HDAC1 reveal molecular determinants of specific complex assembly and their requirement for gene regulation.Nucleic acids research · 2025Article
- Structures and dynamics of Rpd3S complex bound to nucleosome.Science advances · 2024Article
- Article
- Structure of the complete Saccharomyces cerevisiae Rpd3S-nucleosome complex.Nature communications · 2023Article
- Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex.Cell research · 2023Article
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Authors and funding
7 authors at 1 institution in 2 countries.
Funding
Abstract
The Rpd3L histone deacetylase (HDAC) complex is an ancient 12-subunit complex conserved in a broad range of eukaryotes that performs localized deacetylation at or near sites of recruitment by DNA-bound factors. Here we describe the cryo-EM structure of this prototypical HDAC complex that is characterized by as many as seven subunits performing scaffolding roles for the tight integration of the only catalytic subunit, Rpd3. The principal scaffolding protein, Sin3, along with Rpd3 and the histone chaperone, Ume1, are present in two copies, with each copy organized into separate lobes of an asymmetric dimeric molecular assembly. The active site of one Rpd3 is completely occluded by a leucine side chain of Rxt2, while the tips of the two lobes and the more peripherally associated subunits exhibit varying levels of flexibility and positional disorder. The structure reveals unexpected structural homology/analogy between unrelated subunits in the fungal and mammalian complexes and provides a foundation for deeper interrogations of structure, biology, and mechanism of these complexes, as well as for the discovery of HDAC complex-specific inhibitors.
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