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Structure paper

TitleStructures and dynamics of Rpd3S complex bound to nucleosome.
Journal, issue, pagesSci Adv, Vol. 10, Issue 15, Page eadk7678, Year 2024
Publish dateApr 12, 2024
AuthorsChengcheng Wang / Chen Chu / Zhouyan Guo / Xiechao Zhan /
PubMed AbstractThe Rpd3S complex plays a pivotal role in facilitating local histone deacetylation in the transcribed regions to suppress intragenic transcription initiation. Here, we present the cryo-electron ...The Rpd3S complex plays a pivotal role in facilitating local histone deacetylation in the transcribed regions to suppress intragenic transcription initiation. Here, we present the cryo-electron microscopy structures of the budding yeast Rpd3S complex in both its apo and three nucleosome-bound states at atomic resolutions, revealing the exquisite architecture of Rpd3S to well accommodate a mononucleosome without linker DNA. The Rpd3S core, containing a Sin3 Lobe and two NB modules, is a rigid complex and provides three positive-charged anchors (Sin3_HCR and two Rco1_NIDs) to connect nucleosomal DNA. In three nucleosome-bound states, the Rpd3S core exhibits three distinct orientations relative to the nucleosome, assisting the sector-shaped deacetylase Rpd3 to locate above the SHL5-6, SHL0-1, or SHL2-3, respectively. Our work provides a structural framework that reveals a dynamic working model for the Rpd3S complex to engage diverse deacetylation sites.
External linksSci Adv / PubMed:38598631 / PubMed Central
MethodsEM (single particle)
Resolution2.9 - 4.4 Å
Structure data

37364

8w9c

EMDB-37364, PDB-8w9c:
Cryo-EM structure of the Rpd3S complex from budding yeast
Method: EM (single particle) / Resolution: 3.3 Å

37365

8w9d

EMDB-37365, PDB-8w9d:
Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1
Method: EM (single particle) / Resolution: 3.9 Å

37366

8w9e

EMDB-37366, PDB-8w9e:
Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2
Method: EM (single particle) / Resolution: 3.6 Å

37367

8w9f

EMDB-37367, PDB-8w9f:
Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3
Method: EM (single particle) / Resolution: 4.4 Å

EMDB-37368: Cryo-EM map of the Rpd3S region of Rpd3S-nucleosome complex in State1
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-37369: Cryo-EM map of the nucleosome region of Rpd3S-nucleosome complex in State 1
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-37370: Cryo-EM map of the Rpd3S region of Rpd3S-Nulceosome complex in State 2
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-37371: Cryo-EM map of the nucleosome region of Rpd3S-nucleosome complex in State 2
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-37372: Cryo-EM map of the Rpd3S region of Rpd3S-nucleosome complex in State 3
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-37373: Cryo-EM map of the nucleosome region of Rpd3S-nucleosome complex in State 3
Method: EM (single particle) / Resolution: 3.2 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-K:
Unknown entry

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • homo sapiens (human)
KeywordsDNA BINDING PROTEIN / Rpd3S / HDAC / Sin3 / Rpd3 / DNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA COMPLEX

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