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- PDB-7yi5: Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yi5 | |||||||||||||||
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Title | Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in loose state | |||||||||||||||
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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 | ![]() ![]() ![]() ![]() ![]() synthetic construct (others) | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Li, H.T. / Yan, C.Y. / Guan, H.P. / Wang, P. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Diverse modes of H3K36me3-guided nucleosomal deacetylation by Rpd3S. Authors: Haipeng Guan / Pei Wang / Pei Zhang / Chun Ruan / Yutian Ou / Bo Peng / Xiangdong Zheng / Jianlin Lei / Bing Li / Chuangye Yan / Haitao Li / ![]() Abstract: Context-dependent dynamic histone modifications constitute a key epigenetic mechanism in gene regulation. The Rpd3 small (Rpd3S) complex recognizes histone H3 trimethylation on lysine 36 (H3K36me3) ...Context-dependent dynamic histone modifications constitute a key epigenetic mechanism in gene regulation. The Rpd3 small (Rpd3S) complex recognizes histone H3 trimethylation on lysine 36 (H3K36me3) and deacetylates histones H3 and H4 at multiple sites across transcribed regions. Here we solved the cryo-electron microscopy structures of Saccharomyces cerevisiae Rpd3S in its free and H3K36me3 nucleosome-bound states. We demonstrated a unique architecture of Rpd3S, in which two copies of Eaf3-Rco1 heterodimers are asymmetrically assembled with Rpd3 and Sin3 to form a catalytic core complex. Multivalent recognition of two H3K36me3 marks, nucleosomal DNA and linker DNAs by Eaf3, Sin3 and Rco1 positions the catalytic centre of Rpd3 next to the histone H4 N-terminal tail for deacetylation. In an alternative catalytic mode, combinatorial readout of unmethylated histone H3 lysine 4 and H3K36me3 by Rco1 and Eaf3 directs histone H3-specific deacetylation except for the registered histone H3 acetylated lysine 9. Collectively, our work illustrates dynamic and diverse modes of multivalent nucleosomal engagement and methylation-guided deacetylation by Rpd3S, highlighting the exquisite complexity of epigenetic regulation with delicately designed multi-subunit enzymatic machineries in transcription and beyond. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 627.9 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 33852MC ![]() 7yi0C ![]() 7yi1C ![]() 7yi2C ![]() 7yi3C ![]() 7yi4C C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Transcriptional regulatory protein ... , 2 types, 3 molecules ADF
#1: Protein | Mass: 175047.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#4: Protein | Mass: 78951.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
-Protein , 6 types, 11 molecules BCEHLIMJNGK
#2: Protein | Mass: 48961.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||
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#3: Protein | Mass: 45266.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #5: Protein | ![]() Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #6: Protein | ![]() Mass: 13978.241 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #7: Protein | Mass: 13524.752 Da / Num. of mol.: 2 / Mutation: S29T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #10: Protein | ![]() Mass: 15346.010 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: LOC108703785, LOC121398065, LOC121398067, XELAEV_18002543mg Production host: synthetic construct (others) / References: UniProt: A0A310TTQ1 |
-Wisdom 601 DNA (167- ... , 2 types, 2 molecules OP
#8: DNA chain | Mass: 51308.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
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#9: DNA chain | Mass: 51798.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
-Non-polymers , 1 types, 5 molecules ![](data/chem/img/ZN.gif)
#11: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
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Molecular weight | Value: 723 kDa/nm / Experimental value: NO | ||||||||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||||||||
Specimen | Conc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||||||||||||||||||
Vitrification![]() | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 89653 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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