Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structure of histone deacetylase complex Rpd3S bound to nucleosome.
Journal, issue, pages	Nat Struct Mol Biol, Vol. 30, Issue 12, Page 1893-1901, Year 2023
Publish date	Oct 5, 2023
Authors	Wulong Li / Hengjun Cui / Zhimin Lu / Haibo Wang /
PubMed Abstract	Crosstalk between histone modifications represents a fundamental epigenetic mechanism in gene regulation. During the transcription elongation process, the histone deacetylase complex Rpd3S is ...Crosstalk between histone modifications represents a fundamental epigenetic mechanism in gene regulation. During the transcription elongation process, the histone deacetylase complex Rpd3S is recruited to H3K36-methylated nucleosomes to suppress cryptic transcription initiation. However, how subunits of Rpd3S are assembled and coordinated to recognize nucleosomal substrates and exert their deacetylation function remains unclear. Here we report the structure of Saccharomyces cerevisiae Rpd3S deacetylase bound to H3K36me3-modified nucleosome at 3.1 Å resolution. It shows that Sin3 and Rco1 subunits orchestrate the assembly of the complex and mediate its contact with nucleosome at multiple sites, with the Sin3-DNA interface as a pivotal anchor. The PHD1 domain of Rco1 recognizes the unmodified H3K4 and places the following H3 tail toward the active site of Rpd3, while the chromodomain of Eaf3 subunit recognizes the H3K36me3 mark and contacts both nucleosomal and linker DNA. The second copy of Eaf3-Rco1 is involved in neighboring nucleosome binding. Our work unravels the structural basis of chromatin targeting and deacetylation by the Rpd3S complex.
External links	Nat Struct Mol Biol / PubMed:37798513
Methods	EM (single particle)
Resolution	3.0 - 7.6 Å
Structure data	35081 8hxx EMDB-35081, PDB-8hxx: Cryo-EM structure of the histone deacetylase complex Rpd3S Method: EM (single particle) / Resolution: 3.0 Å 35082 8hxy EMDB-35082, PDB-8hxy: Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Method: EM (single particle) / Resolution: 3.1 Å 35083 8hxz EMDB-35083, PDB-8hxz: Cryo-EM structure of Eaf3 CHD in complex with nucleosome Method: EM (single particle) / Resolution: 3.4 Å 35084 8hy0 EMDB-35084, PDB-8hy0: Composite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Method: EM (single particle) / Resolution: 3.1 Å EMDB-35217: Concensus map of the Rpd3S-nucleosome complex Method: EM (single particle) / Resolution: 3.7 Å EMDB-35218: Focused refinement map of nucleosome in the Rpd3S-nucleosome complex Method: EM (single particle) / Resolution: 3.2 Å EMDB-35219: Focused refinement map of Rpd3S in the Rpd3S-nucleosome complex Method: EM (single particle) / Resolution: 3.1 Å EMDB-35220: Focused refinement map of the tail of Rpd3S Method: EM (single particle) / Resolution: 3.4 Å EMDB-35221: Focused refinement map of the CHD of Eaf3 in the Rpd3S-nucleosome complex Method: EM (single particle) / Resolution: 3.9 Å 36283 8jho EMDB-36283, PDB-8jho: Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome Method: EM (single particle) / Resolution: 7.6 Å
Chemicals	ChemComp-ZN: Unknown entry
Source	saccharomyces cerevisiae (brewer's yeast) xenopus laevis (African clawed frog) synthetic construct (others) Saccharomyces (fungus)
Keywords	GENE REGULATION / Histone deacetylase complex / Rpd3S-nucleosome complex / Histone deacetylation / Histone modification binding domain / nucleosome / HDAC / di-nucleosome