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- EMDB-35084: Composite cryo-EM structure of the histone deacetylase complex Rp... -
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Open data
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Basic information
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Title | Composite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome | |||||||||
![]() | Composite EM map | |||||||||
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![]() | Histone deacetylase complex / nucleosome / GENE REGULATION | |||||||||
Function / homology | ![]() Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / protein localization to nucleolar rDNA repeats / negative regulation of rDNA heterochromatin formation / Rpd3S complex / Rpd3L complex / Rpd3L-Expanded complex / rDNA chromatin condensation / nucleophagy ...Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / protein localization to nucleolar rDNA repeats / negative regulation of rDNA heterochromatin formation / Rpd3S complex / Rpd3L complex / Rpd3L-Expanded complex / rDNA chromatin condensation / nucleophagy / HDACs deacetylate histones / NuRD complex / histone deacetylase / SUMOylation of chromatin organization proteins / regulation of DNA-templated DNA replication initiation / negative regulation of transcription by RNA polymerase I / histone deacetylase activity / Sin3-type complex / NuA4 histone acetyltransferase complex / Estrogen-dependent gene expression / histone deacetylase complex / positive regulation of macroautophagy / nuclear periphery / transcription elongation by RNA polymerase II / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / response to oxidative stress / transcription coactivator activity / chromatin remodeling / cell cycle / protein heterodimerization activity / cell division / DNA repair / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Cui H / Wang H | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of histone deacetylase complex Rpd3S bound to nucleosome. Authors: Wulong Li / Hengjun Cui / Zhimin Lu / Haibo Wang / ![]() 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. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 47 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 31.1 KB 31.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.1 KB | Display | ![]() |
Images | ![]() | 177.2 KB | ||
Filedesc metadata | ![]() | 9.3 KB | ||
Others | ![]() ![]() | 59.1 MB 59 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 715.6 KB | Display | ![]() |
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Full document | ![]() | 715.2 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hy0MC ![]() 8hxxC ![]() 8hxyC ![]() 8hxzC ![]() 8jhoC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Composite EM map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Composite EM half2 map
File | emd_35084_half_map_1.map | ||||||||||||
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Annotation | Composite EM half2 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Composite EM half2 map
File | emd_35084_half_map_2.map | ||||||||||||
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Annotation | Composite EM half2 map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Rpd3S histone deacetylase in complex with nucleosome
+Supramolecule #1: Rpd3S histone deacetylase in complex with nucleosome
+Macromolecule #1: Histone H3
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A
+Macromolecule #4: Histone H2B
+Macromolecule #7: Transcriptional regulatory protein SIN3
+Macromolecule #8: Histone deacetylase RPD3
+Macromolecule #9: Chromatin modification-related protein EAF3
+Macromolecule #10: RCO1 isoform 1
+Macromolecule #5: DNA (352-MER)
+Macromolecule #6: DNA (352-MER)
+Macromolecule #11: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 Details: 20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 44.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-8hy0: |