8KC7

Rpd3S histone deacetylase complex

• PDB DOI:  https://doi.org/10.2210/pdb8KC7/pdb
• EM Map EMD-37096: EMDB EMDataResource

• Classification: TRANSCRIPTION
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2023-08-06 Released: 2023-09-13 
• Deposition Author(s): 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.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.46 Å
• Aggregation State: 3D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex.

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.

(2023) Cell Res 

• PubMed: 37666978 
• DOI: https://doi.org/10.1038/s41422-023-00869-1
• Primary Citation of Related Structures:  
  8KC7, 8KD2, 8KD3, 8KD4, 8KD5, 8KD6, 8KD7


• 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.

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Organizational Affiliation: 

Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B1C1D1E1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 466.02 kDa 
• Atom Count: 14,326 
• Modelled Residue Count: 1,748 
• Deposited Residue Count: 4,072 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase RPD3	A	433	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPD3, MOF6, REC3, SDI2, SDS6, YNL330C, N0305 EC: 3.5.1.98
UniProt
Find proteins for P32561 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32561  Go to UniProtKB:  P32561

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulatory protein SIN3	B	1,371	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SIN3, CPE1, GAM2, RPD1, SDI1, SDS16, UME4, YOL004W
UniProt
Find proteins for P22579 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22579  Go to UniProtKB:  P22579

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin modification-related protein EAF3	C [auth D], E [auth F]	401	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: EAF3, YPR023C, YP9367.03C
UniProt
Find proteins for Q12432 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12432  Go to UniProtKB:  Q12432

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulatory protein RCO1	D [auth E], F [auth G]	733	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RCO1, YMR075W, YM9916.14
UniProt
Find proteins for Q04779 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04779  Go to UniProtKB:  Q04779

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.46 Å
• Aggregation State: 3D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-13 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	NSFC U20A2013
National Natural Science Foundation of China (NSFC)	China	32241021
National Natural Science Foundation of China (NSFC)	China	32170189
Other government		MYRG2018-00221-FHS
Other government		0009/2018/A1
Other government		0032/2021/A1
Other government		202102080156
Other government		2019QN01Y051

Revision History  

• Version 1.0: 2023-09-13
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Database references