8KD5

Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2

Summary for 8KD5

• Entry DOI: 10.2210/pdb8kd5/pdb
• EMDB information: 37125
• Descriptor: Chromatin modification-related protein EAF3, Transcriptional regulatory protein RCO1, ZINC ION, ... (11 entities in total)
• Functional Keywords: rpd3s, hdac, hho1, cryptic transcription, transcription
• Biological source: Saccharomyces cerevisiae (baker's yeast); More
• Total number of polymer chains: 16
• Total formula weight: 697250.98

Authors

Dong, S.,Li, H.,Wang, M.,Rasheed, N.,Zou, B.,Gao, X.,Guan, J.,Li, W.,Zhang, J.,Wang, C.,Zhou, N.,Shi, X.,Li, M.,Zhou, M.,Huang, J.,Li, H.,Zhang, Y.,Wong, K.H.,Chang, X.,Chao, W.C.H.,He, J. (deposition date: 2023-08-09, release date: 2023-09-13, Last modification date: 2023-10-11)

Primary citation

Dong, S.,Li, H.,Wang, M.,Rasheed, N.,Zou, B.,Gao, X.,Guan, J.,Li, W.,Zhang, J.,Wang, C.,Zhou, N.,Shi, X.,Li, M.,Zhou, M.,Huang, J.,Li, H.,Zhang, Y.,Wong, K.H.,Zhang, X.,Chao, W.C.H.,He, J.
Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex.
Cell Res., 33:790-801, 2023

PubMed Abstract: In Saccharomyces cerevisiae, cryptic transcription at the coding region is prevented by the activity of Sin3 histone deacetylase (HDAC) complex Rpd3S, which is carried by the transcribing RNA polymerase II (RNAPII) to deacetylate and stabilize chromatin. Despite its fundamental importance, the mechanisms by which Rpd3S deacetylates nucleosomes and regulates chromatin dynamics remain elusive. Here, we determined several cryo-EM structures of Rpd3S in complex with nucleosome core particles (NCPs), including the H3/H4 deacetylation states, the alternative deacetylation state, the linker tightening state, and a state in which Rpd3S co-exists with the Hho1 linker histone on NCP. These structures suggest that Rpd3S utilizes a conserved Sin3 basic surface to navigate through the nucleosomal DNA, guided by its interactions with H3K36 methylation and the extra-nucleosomal DNA linkers, to target acetylated H3K9 and sample other histone tails. Furthermore, our structures illustrate that Rpd3S reconfigures the DNA linkers and acts in concert with Hho1 to engage the NCP, potentially unraveling how Rpd3S and Hho1 work in tandem for gene silencing.

PubMed: 37666978
DOI: 10.1038/s41422-023-00869-1

Experimental method

ELECTRON MICROSCOPY (2.9 Å)