8KD7

Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.09 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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 33: 790-801

  • 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.


  • Organizational Affiliation

    CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase RPD3433Saccharomyces cerevisiaeMutation(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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UniProt GroupP32561
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulatory protein SIN31,371Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SIN3CPE1GAM2RPD1SDI1SDS16UME4YOL004W
UniProt
Find proteins for P22579 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin modification-related protein EAF3C [auth D],
E [auth F]
401Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: EAF3
UniProt
Find proteins for Q12432 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulatory protein RCO1D [auth E],
F [auth G]
733Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RCO1
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3G [auth O],
K [auth S]
135Xenopus laevisMutation(s): 1 
Gene Names: LOC121398065
UniProt
Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4H [auth P],
L [auth T]
102Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2AI [auth Q],
M [auth U]
129Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591XELAEV_18003602mg
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1J [auth R],
N [auth V]
122Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P02281 (Xenopus laevis)
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Entity ID: 9
MoleculeChains LengthOrganismImage
167bp DNAO [auth X]167synthetic construct
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Entity ID: 10
MoleculeChains LengthOrganismImage
167bp DNAP [auth Y]167synthetic construct
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Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M3L
Query on M3L
G [auth O],
K [auth S]
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.09 Å
  • Aggregation State: 3D ARRAY 
  • 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)ChinaNSFC U20A2013
National Natural Science Foundation of China (NSFC)China32241021
National Natural Science Foundation of China (NSFC)China32170189
Other governmentMYRG2018-00221-FHS
Other government0009/2018/A1
Other government0032/2021/A1
Other government202102080156
Other government2019QN01Y051

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-13
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Database references