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- EMDB-37126: Rpd3S in complex with nucleosome with H3K36MLA modification and 1... -
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Open data
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Basic information
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Title | Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3 | |||||||||||||||||||||||||||
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![]() | Rpd3S / HDAC / Hho1 / cryptic transcription / TRANSCRIPTION | |||||||||||||||||||||||||||
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 / Rpd3L complex / protein localization to nucleolar rDNA repeats / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / Rpd3S 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 / Rpd3L complex / protein localization to nucleolar rDNA repeats / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / Rpd3S complex / rDNA chromatin condensation / regulation of RNA stability / nucleophagy / HDACs deacetylate histones / DNA replication-dependent chromatin assembly / histone deacetylase / cellular response to nitrogen starvation / SUMOylation of chromatin organization proteins / nucleosome disassembly / regulation of DNA-templated DNA replication initiation / negative regulation of transcription by RNA polymerase I / histone deacetylase activity / NuA4 histone acetyltransferase complex / Sin3-type complex / Estrogen-dependent gene expression / histone deacetylase complex / positive regulation of macroautophagy / histone acetyltransferase complex / methylated histone binding / nuclear periphery / meiotic cell cycle / positive regulation of transcription elongation by RNA polymerase II / 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 / protein heterodimerization activity / cell division / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription / 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: 3.07 Å | |||||||||||||||||||||||||||
![]() | Dong S / Li H / Wang M / Rasheed N / Zou B / Gao X / Guan J / Li W / Zhang J / Wang C ...Dong S / Li H / Wang M / Rasheed N / Zou B / Gao X / Guan J / Li W / Zhang J / Wang C / Zhou N / Shi X / Li M / Zhou M / Huang J / Zhang Y / Wong KH / Zhang X / Chao WCH / He J | |||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex. Authors: Shuqi Dong / Huadong Li / Meilin Wang / Nadia Rasheed / Binqian Zou / Xijie Gao / Jiali Guan / Weijie Li / Jiale Zhang / Chi Wang / Ningkun Zhou / Xue Shi / Mei Li / Min Zhou / Junfeng Huang ...Authors: Shuqi Dong / Huadong Li / Meilin Wang / Nadia Rasheed / Binqian Zou / Xijie Gao / Jiali Guan / Weijie Li / Jiale Zhang / Chi Wang / Ningkun Zhou / Xue Shi / Mei Li / Min Zhou / Junfeng Huang / He Li / Ying Zhang / Koon Ho Wong / Xiaofei Zhang / William Chong Hang Chao / Jun He / ![]() Abstract: In Saccharomyces cerevisiae, cryptic transcription at the coding region is prevented by the activity of Sin3 histone deacetylase (HDAC) complex Rpd3S, which is carried by the transcribing RNA ...In Saccharomyces cerevisiae, cryptic transcription at the coding region is prevented by the activity of Sin3 histone deacetylase (HDAC) complex Rpd3S, which is carried by the transcribing RNA polymerase II (RNAPII) to deacetylate and stabilize chromatin. Despite its fundamental importance, the mechanisms by which Rpd3S deacetylates nucleosomes and regulates chromatin dynamics remain elusive. Here, we determined several cryo-EM structures of Rpd3S in complex with nucleosome core particles (NCPs), including the H3/H4 deacetylation states, the alternative deacetylation state, the linker tightening state, and a state in which Rpd3S co-exists with the Hho1 linker histone on NCP. These structures suggest that Rpd3S utilizes a conserved Sin3 basic surface to navigate through the nucleosomal DNA, guided by its interactions with H3K36 methylation and the extra-nucleosomal DNA linkers, to target acetylated H3K9 and sample other histone tails. Furthermore, our structures illustrate that Rpd3S reconfigures the DNA linkers and acts in concert with Hho1 to engage the NCP, potentially unraveling how Rpd3S and Hho1 work in tandem for gene silencing. | |||||||||||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 295.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 31.6 KB 31.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 24.8 KB | Display | ![]() |
Images | ![]() | 24.4 KB | ||
Masks | ![]() | 600.7 MB | ![]() | |
Filedesc metadata | ![]() | 9.1 KB | ||
Others | ![]() ![]() | 552.7 MB 552.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8kd6MC ![]() 8kc7C ![]() 8kd2C ![]() 8kd3C ![]() 8kd4C ![]() 8kd5C ![]() 8kd7C 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: 0.71 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #2
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
+Entire : H3/H4 deacetylation state of Rpd3S-NCP(187bp/MLA) class3
+Supramolecule #1: H3/H4 deacetylation state of Rpd3S-NCP(187bp/MLA) class3
+Supramolecule #2: Rpd3-Sin3-Eaf3-Rco1
+Supramolecule #3: histone
+Supramolecule #4: DNA
+Macromolecule #1: Chromatin modification-related protein EAF3
+Macromolecule #2: Histone H3
+Macromolecule #3: Histone H4
+Macromolecule #4: Histone H2A
+Macromolecule #5: Histone H2B 1.1
+Macromolecule #8: Histone deacetylase RPD3
+Macromolecule #9: Transcriptional regulatory protein SIN3
+Macromolecule #10: Transcriptional regulatory protein RCO1
+Macromolecule #6: 187bp DNA
+Macromolecule #7: 187bp DNA
+Macromolecule #11: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | 3D array |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |