Molecular basis for Eaf3-mediated assembly of Rpd3S and NuA4

Chen, Zhenzhen; Lundy, Taylor A.; Zhu, Zhongliang; Hoskins, Victoria E.; Zhang, Jiahai; Yao, Xuebiao; Strahl, Brian D.; Xu, Chao

doi:10.1038/s41421-023-00565-9

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2024

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“…S10). It is consistent with the previous reports that the PHD1 of Rco1 recognizes the unmodified N terminus of H3 ( 29 – 31 ). Furthermore, our cryo-EM analysis reveals an extra density for a peptide with a long sidechain extended into the pocket of the active site in state 1 ( Fig.…”

Section: Resultssupporting

confidence: 93%

Structures and dynamics of Rpd3S complex bound to nucleosome

Wang,

Chu,

Guo

et al. 2024

Sci. Adv.

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The Rpd3S complex plays a pivotal role in facilitating local histone deacetylation in the transcribed regions to suppress intragenic transcription initiation. Here, we present the cryo–electron microscopy structures of the budding yeast Rpd3S complex in both its apo and three nucleosome-bound states at atomic resolutions, revealing the exquisite architecture of Rpd3S to well accommodate a mononucleosome without linker DNA. The Rpd3S core, containing a Sin3 Lobe and two NB modules, is a rigid complex and provides three positive-charged anchors (Sin3_HCR and two Rco1_NIDs) to connect nucleosomal DNA. In three nucleosome-bound states, the Rpd3S core exhibits three distinct orientations relative to the nucleosome, assisting the sector-shaped deacetylase Rpd3 to locate above the SHL5-6, SHL0-1, or SHL2-3, respectively. Our work provides a structural framework that reveals a dynamic working model for the Rpd3S complex to engage diverse deacetylation sites.

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Section: Resultssupporting

confidence: 93%