8W9C
Cryo-EM structure of the Rpd3S complex from budding yeast
Summary for 8W9C
| Entry DOI | 10.2210/pdb8w9c/pdb |
| EMDB information | 37364 |
| Descriptor | Transcriptional regulatory protein SIN3, Transcriptional regulatory protein RCO1, Histone deacetylase RPD3, ... (6 entities in total) |
| Functional Keywords | rpd3s, hdac, sin3, rpd3, dna binding protein |
| Biological source | Saccharomyces cerevisiae (brewer's yeast) More |
| Total number of polymer chains | 6 |
| Total formula weight | 472980.70 |
| Authors | |
| 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 Cited by 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: 38598631DOI: 10.1126/sciadv.adk7678 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.3 Å) |
Structure validation
Download full validation report
