7YI3

Cryo-EM structure of Rpd3S in close-state Rpd3S-NCP complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Diverse modes of H3K36me3-guided nucleosomal deacetylation by Rpd3S.

Guan, H.Wang, P.Zhang, P.Ruan, C.Ou, Y.Peng, B.Zheng, X.Lei, J.Li, B.Yan, C.Li, H.

(2023) Nature 620: 669-675

  • DOI: https://doi.org/10.1038/s41586-023-06349-1
  • Primary Citation of Related Structures:  
    7YI0, 7YI1, 7YI2, 7YI3, 7YI4, 7YI5

  • PubMed Abstract: 

    Context-dependent dynamic histone modifications constitute a key epigenetic mechanism in gene regulation 1-4 . The Rpd3 small (Rpd3S) complex recognizes histone H3 trimethylation on lysine 36 (H3K36me3) and deacetylates histones H3 and H4 at multiple sites across transcribed regions 5-7 . Here we solved the cryo-electron microscopy structures of Saccharomyces cerevisiae Rpd3S in its free and H3K36me3 nucleosome-bound states. We demonstrated a unique architecture of Rpd3S, in which two copies of Eaf3-Rco1 heterodimers are asymmetrically assembled with Rpd3 and Sin3 to form a catalytic core complex. Multivalent recognition of two H3K36me3 marks, nucleosomal DNA and linker DNAs by Eaf3, Sin3 and Rco1 positions the catalytic centre of Rpd3 next to the histone H4 N-terminal tail for deacetylation. In an alternative catalytic mode, combinatorial readout of unmethylated histone H3 lysine 4 and H3K36me3 by Rco1 and Eaf3 directs histone H3-specific deacetylation except for the registered histone H3 acetylated lysine 9. Collectively, our work illustrates dynamic and diverse modes of multivalent nucleosomal engagement and methylation-guided deacetylation by Rpd3S, highlighting the exquisite complexity of epigenetic regulation with delicately designed multi-subunit enzymatic machineries in transcription and beyond.


  • Organizational Affiliation

    State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulatory protein SIN31,536Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SIN3
UniProt
Find proteins for P22579 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P22579
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UniProt GroupP22579
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase RPD3433Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPD3
EC: 3.5.1.98
UniProt
Find proteins for P32561 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P32561
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UniProt GroupP32561
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin modification-related protein EAF3401Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EAF3
UniProt
Find proteins for Q12432 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q12432
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UniProt GroupQ12432
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulatory protein RCO1
D, E
684Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RCO1
UniProt
Find proteins for Q04779 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04779 
Go to UniProtKB:  Q04779
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UniProt GroupQ04779
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31725014
National Natural Science Foundation of China (NSFC)China91753203
Ministry of Science and Technology (MoST, China)China2020YFA0803300
Ministry of Science and Technology (MoST, China)China2021YFA1300100

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2023-08-02
    Changes: Database references
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references