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- EMDB-37127: 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 167bp DNA | |||||||||||||||||||||||||||
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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 / Rpd3L complex / Rpd3S complex / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation ...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 / Rpd3L complex / Rpd3S complex / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / 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 | ![]() ![]() | |||||||||||||||||||||||||||
![]() | 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 / Chang 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 | ![]() | 284.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 31.3 KB 31.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 24.8 KB | Display | ![]() |
Images | ![]() | 25.6 KB | ||
Masks | ![]() | 600.7 MB | ![]() | |
Filedesc metadata | ![]() | 9 KB | ||
Others | ![]() ![]() | 552.9 MB 552.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8kd7MC ![]() 8kc7C ![]() 8kd2C ![]() 8kd3C ![]() 8kd4C ![]() 8kd5C ![]() 8kd6C 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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-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 : Alternative deacetylation state of Rpd3S-NCP(167bp/MLA)
+Supramolecule #1: Alternative deacetylation state of Rpd3S-NCP(167bp/MLA)
+Supramolecule #2: Eaf3-Rpd3-Sin3
+Supramolecule #3: Histone
+Supramolecule #4: 167bp DNA
+Macromolecule #1: Histone deacetylase RPD3
+Macromolecule #2: Transcriptional regulatory protein SIN3
+Macromolecule #3: Chromatin modification-related protein EAF3
+Macromolecule #4: Transcriptional regulatory protein RCO1
+Macromolecule #5: Histone H3
+Macromolecule #6: Histone H4
+Macromolecule #7: Histone H2A
+Macromolecule #8: Histone H2B 1.1
+Macromolecule #9: 167bp DNA
+Macromolecule #10: 167bp DNA
-Experimental details
-Structure determination
Method | ![]() |
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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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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |