8TOF

Rpd3S bound to an H3K36Cme3 modified nucleosome

Summary for 8TOF

• Entry DOI: 10.2210/pdb8tof/pdb
• EMDB information: 41449
• Descriptor: Transcriptional regulatory protein SIN3, Histone H2A, Histone H2B 1.1, ... (13 entities in total)
• Functional Keywords: nucleosome, methylation, acetylation, rpd3s, transcription, transcription-dna complex, transcription/dna
• Biological source: Saccharomyces cerevisiae (baker's yeast); More
• Total number of polymer chains: 18
• Total formula weight: 713284.07

Authors

Markert, J.W.,Vos, S.M.,Farnung, L. (deposition date: 2023-08-03, release date: 2024-01-17, Last modification date: 2024-11-06)

Primary citation

Markert, J.W.,Vos, S.M.,Farnung, L.
Structure of the complete Saccharomyces cerevisiae Rpd3S-nucleosome complex.
Nat Commun, 14:8128-8128, 2023

PubMed Abstract: Acetylation of histones is a key post-translational modification that guides gene expression regulation. In yeast, the class I histone deacetylase containing Rpd3S complex plays a critical role in the suppression of spurious transcription by removing histone acetylation from actively transcribed genes. The S. cerevisiae Rpd3S complex has five subunits (Rpd3, Sin3, Rco1, Eaf3, and Ume1) but its subunit stoichiometry and how the complex engages nucleosomes to achieve substrate specificity remains elusive. Here we report the cryo-EM structure of the complete Rpd3S complex bound to a nucleosome. Sin3 and two copies of subunits Rco1 and Eaf3 encircle the deacetylase subunit Rpd3 and coordinate the positioning of Ume1. The Rpd3S complex binds both trimethylated H3 tails at position lysine 36 and makes multiple additional contacts with the nucleosomal DNA and the H2A-H2B acidic patch. Direct regulation via the Sin3 subunit coordinates binding of the acetylated histone substrate to achieve substrate specificity.

PubMed: 38065958
DOI: 10.1038/s41467-023-43968-8

Experimental method

ELECTRON MICROSCOPY (2.8 Å)