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Yorodumi- EMDB-36283: Cryo-EM structure of the histone deacetylase complex Rpd3S in com... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36283 | |||||||||
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Title | Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome | |||||||||
Map data | global refinement map | |||||||||
Sample |
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Keywords | HDAC / di-nucleosome / GENE REGULATION | |||||||||
Function / homology | Function and homology information Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / Rpd3L complex / protein localization to nucleolar rDNA repeats / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / Rpd3S complex / rDNA chromatin condensation / nucleophagy ...Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / Rpd3L complex / protein localization to nucleolar rDNA repeats / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / Rpd3S complex / rDNA chromatin condensation / nucleophagy / HDACs deacetylate histones / histone deacetylase / SUMOylation of chromatin organization proteins / cellular response to nitrogen starvation / negative regulation of transcription by RNA polymerase I / regulation of DNA-templated DNA replication initiation / histone deacetylase activity / NuA4 histone acetyltransferase complex / Sin3-type complex / Estrogen-dependent gene expression / histone deacetylase complex / positive regulation of macroautophagy / nuclear periphery / meiotic cell cycle / transcription elongation by RNA polymerase II / heterochromatin formation / double-strand break repair via nonhomologous end joining / G1/S transition of mitotic cell cycle / structural constituent of chromatin / transcription corepressor activity / G2/M transition of mitotic cell cycle / nucleosome / nucleosome assembly / cellular response to heat / response to oxidative stress / transcription coactivator activity / chromatin remodeling / 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 | Xenopus laevis (African clawed frog) / Saccharomyces cerevisiae (brewer's yeast) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.6 Å | |||||||||
Authors | Wang H | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 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 | emd_36283.map.gz | 195 MB | EMDB map data format | |
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Header (meta data) | emd-36283-v30.xml emd-36283.xml | 35 KB 35 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36283_fsc.xml | 14.3 KB | Display | FSC data file |
Images | emd_36283.png | 131 KB | ||
Filedesc metadata | emd-36283.cif.gz | 9.4 KB | ||
Others | emd_36283_additional_1.map.gz emd_36283_half_map_1.map.gz emd_36283_half_map_2.map.gz | 100.3 MB 195.8 MB 195.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36283 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36283 | HTTPS FTP |
-Validation report
Summary document | emd_36283_validation.pdf.gz | 725 KB | Display | EMDB validaton report |
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Full document | emd_36283_full_validation.pdf.gz | 724.5 KB | Display | |
Data in XML | emd_36283_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | emd_36283_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36283 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36283 | HTTPS FTP |
-Related structure data
Related structure data | 8jhoMC 8hxxC 8hxyC 8hxzC 8hy0C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_36283.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | global refinement map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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
-Additional map: composite map
File | emd_36283_additional_1.map | ||||||||||||
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Annotation | composite map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_36283_half_map_1.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_36283_half_map_2.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Rpd3S histone deacetylase in complex with di-nucleosome
+Supramolecule #1: Rpd3S histone deacetylase in complex with di-nucleosome
+Supramolecule #2: di-nucleosome
+Supramolecule #3: The Rpd3S HDAC complex
+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: Di-nucleosome template foward
+Macromolecule #6: Di-nucleosome template reverse
+Macromolecule #11: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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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Grid | Model: Quantifoil R2/2 / Material: GOLD / Mesh: 200 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-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: FIELD EMISSION GUN |
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 |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-8jho: |