8W9E

Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2

Summary for 8W9E

• Entry DOI: 10.2210/pdb8w9e/pdb
• EMDB information: 37366
• Descriptor: Transcriptional regulatory protein SIN3, 3-DNA, ZINC ION, ... (12 entities in total)
• Functional Keywords: rpd3s, hdac, sin3, rpd3, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Saccharomyces cerevisiae (baker's yeast); More
• Total number of polymer chains: 17
• Total formula weight: 718771.81

Authors

Wang, C.,Zhan, X. (deposition date: 2023-09-05, release date: 2024-05-15)

Primary citation

Wang, C.,Chu, C.,Guo, Z.,Zhan, X.
Structures and dynamics of Rpd3S complex bound to nucleosome.
Sci Adv, 10:eadk7678-eadk7678, 2024

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 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.

PubMed: 38598631
DOI: 10.1126/sciadv.adk7678

Experimental method

ELECTRON MICROSCOPY (3.6 Å)