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-Structure paper
Title | Structures and dynamics of Rpd3S complex bound to nucleosome. |
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Journal, issue, pages | Sci Adv, Vol. 10, Issue 15, Page eadk7678, Year 2024 |
Publish date | Apr 12, 2024 |
Authors | Chengcheng Wang / Chen Chu / Zhouyan Guo / Xiechao Zhan / |
PubMed Abstract | 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 ...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. |
External links | Sci Adv / PubMed:38598631 / PubMed Central |
Methods | EM (single particle) |
Resolution | 2.9 - 4.4 Å |
Structure data | EMDB-37364, PDB-8w9c: EMDB-37365, PDB-8w9d: EMDB-37366, PDB-8w9e: EMDB-37367, PDB-8w9f: EMDB-37368: Cryo-EM map of the Rpd3S region of Rpd3S-nucleosome complex in State1 EMDB-37369: Cryo-EM map of the nucleosome region of Rpd3S-nucleosome complex in State 1 EMDB-37370: Cryo-EM map of the Rpd3S region of Rpd3S-Nulceosome complex in State 2 EMDB-37371: Cryo-EM map of the nucleosome region of Rpd3S-nucleosome complex in State 2 EMDB-37372: Cryo-EM map of the Rpd3S region of Rpd3S-nucleosome complex in State 3 EMDB-37373: Cryo-EM map of the nucleosome region of Rpd3S-nucleosome complex in State 3 |
Chemicals | ChemComp-ZN: ChemComp-K: |
Source |
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Keywords | DNA BINDING PROTEIN / Rpd3S / HDAC / Sin3 / Rpd3 / DNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA COMPLEX |