Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex

Area of Science:

• Biochemistry
• Structural Biology
• Molecular Biology

Background:

• The Rpd3L histone deacetylase (HDAC) complex is a conserved, ancient, multi-subunit complex found across eukaryotes.
• It plays a crucial role in localized deacetylation, often near DNA-bound factors.
• Understanding its structure is key to elucidating its biological functions.

Purpose of the Study:

• To determine the cryo-electron microscopy (cryo-EM) structure of the Rpd3L HDAC complex.
• To characterize the scaffolding roles of its subunits and the integration of the catalytic subunit, Rpd3.
• To investigate the structural organization and potential regulatory mechanisms within the complex.

Main Methods:

• Cryo-electron microscopy (cryo-EM) was employed to resolve the structure of the Rpd3L HDAC complex.
• Detailed structural analysis was performed to identify subunit interactions and organization.
• Comparative analysis was conducted to identify conserved and divergent features across species.

Main Results:

• The cryo-EM structure reveals a 12-subunit complex with seven subunits acting as scaffolds for the catalytic subunit, Rpd3.
• The complex forms an asymmetric dimeric assembly with two copies of Sin3, Rpd3, and Ume1, organized into separate lobes.
• One Rpd3 active site is occluded by Rxt2, and peripheral subunits show flexibility, suggesting dynamic regulation.

Conclusions:

• The determined structure provides unprecedented insight into the intricate assembly and organization of the Rpd3L HDAC complex.
• Unexpected structural homologies between fungal and mammalian subunits suggest conserved mechanisms.
• This structural foundation facilitates further research into HDAC complex biology, mechanism, and the development of targeted inhibitors.