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- EMDB-37366: Cryo-EM structure of the Rpd3S-nucleosome complex from budding ye... -
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Open data
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Basic information
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Title | Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2 | |||||||||
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![]() | Rpd3S / ![]() | |||||||||
Function / homology | ![]() nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / protein localization to nucleolar rDNA repeats / Rpd3S complex / negative regulation of rDNA heterochromatin formation / Rpd3L complex / Rpd3L-Expanded complex ...nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / protein localization to nucleolar rDNA repeats / Rpd3S complex / negative regulation of rDNA heterochromatin formation / Rpd3L complex / Rpd3L-Expanded complex / rDNA chromatin condensation / regulation of RNA stability / nucleophagy / HDACs deacetylate histones / DNA replication-dependent chromatin assembly / nucleosome disassembly / NuRD complex / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Wang C / Zhan X | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures and dynamics of Rpd3S complex bound to nucleosome. Authors: Chengcheng Wang / Chen Chu / Zhouyan Guo / Xiechao Zhan / ![]() Abstract: 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 ...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. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 78.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.2 KB 24.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10 KB | Display | ![]() |
Images | ![]() | 50.3 KB | ||
Filedesc metadata | ![]() | 8 KB | ||
Others | ![]() ![]() | 65.3 MB 65.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8w9eMC ![]() 8w9cC ![]() 8w9dC ![]() 8w9fC M: atomic model generated by this map C: citing same article ( |
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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
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Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_37366_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37366_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
+Entire : The Rpd3S complex
+Supramolecule #1: The Rpd3S complex
+Macromolecule #1: Transcriptional regulatory protein SIN3
+Macromolecule #2: Transcriptional regulatory protein RCO1
+Macromolecule #3: Histone deacetylase RPD3
+Macromolecule #4: Chromatin modification-related protein EAF3
+Macromolecule #5: Histone H3.1
+Macromolecule #6: Histone H4
+Macromolecule #7: Histone H2A type 1-B/E
+Macromolecule #8: Histone H2B type 1-K
+Macromolecule #9: 5-DNA
+Macromolecule #10: 3-DNA
+Macromolecule #11: ZINC ION
+Macromolecule #12: POTASSIUM ION
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |