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

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.

Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex

“…The recent studies on Rpd3S and Rpd3L revealed the complex assemblies and architecture in their apo states. 29 – 31 Several structural studies have focused on the HDACs’ recognition of nucleosome substrates. 32 , 33 The structure of Sirt6 was believed to be the first HDAC in a complex with an H3 tail substrate in the context of nucleosome.…”

Structure of the complete Saccharomyces cerevisiae Rpd3S-nucleosome complex

“…3b , Supplementary Fig. 5 ), mirroring the interaction seen between Sds3 and the Sin3 HID domain in the Rpd3L complex 18 , 25 . Rco1 A meanders across the surface of Rpd3 via residues 163-190 and complements Rpd3’s β-sheet by contributing an additional β-strand (Rco1 A residues 176-179) (Fig.…”

“…3c ). Notably, in the Rpd3L complex, Dep1 engages in similar contacts across the Rpd3 surface but does not augment the Rpd3 β-sheet 18 , 25 (Supplementary Fig. 5 ).…”

“…While our resolution is currently insufficient for accurate Ume1 positioning, we can clarify its global placement relative to other Rpd3S subunits (Supplementary Table 3 ). Recent structures of Rpd3L and S. pombe Sin3S show that Ume1 is primarily coordinated by the Sin3 HCR domain 18 , 25 . The Ume1-binding part of the Sin3 HCR domain is only flexibly tethered to the Rpd3S core, rationalizing why we can observe Ume1 only at limited resolutions of greater than 8 Å.…”

Structures and dynamics of Rpd3S complex bound to nucleosome

“…Comparing the structures of these complexes in S. cerevisiae , we also find that the Sin3 Lobe of the Rpd3S is much similar with the ARM2 of the Rpd3L (fig. S13A) ( 15 , 16 ). Furthermore, we try to see whether the nucleosome binding mechanism of Rpd3S could partially extend to the Rpd3L complex.…”