+Open data
-Basic information
Entry | Database: PDB / ID: 8hpo | ||||||
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Title | Cryo-EM structure of a SIN3/HDAC complex from budding yeast | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / SIN3 / HDAC / deacetylase / Rpd3 | ||||||
Function / homology | Function and homology information : / regulation of invasive growth in response to glucose limitation / PI5P Regulates TP53 Acetylation / conjugation with cellular fusion / Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / positive regulation of invasive growth in response to glucose limitation / invasive growth in response to glucose limitation / Rpd3L complex ...: / regulation of invasive growth in response to glucose limitation / PI5P Regulates TP53 Acetylation / conjugation with cellular fusion / Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / positive regulation of invasive growth in response to glucose limitation / invasive growth in response to glucose limitation / Rpd3L complex / protein localization to nucleolar rDNA repeats / Rpd3S complex / : / HDACs deacetylate histones / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / regulation of meiotic nuclear division / SUMOylation of transcription cofactors / rDNA chromatin condensation / cell adhesion involved in single-species biofilm formation / nucleophagy / SUMOylation of chromatin organization proteins / histone deacetylase / regulation of DNA-templated DNA replication initiation / negative regulation of transcription by RNA polymerase I / histone deacetylase activity / Sin3-type complex / positive regulation of macroautophagy / histone deacetylase complex / heterochromatin formation / methylated histone binding / nuclear periphery / meiotic cell cycle / transcription elongation by RNA polymerase II / transcription coregulator activity / nucleosome assembly / double-strand break repair via nonhomologous end joining / histone deacetylase binding / transcription corepressor activity / chromatin organization / histone binding / response to oxidative stress / transcription coactivator activity / chromatin remodeling / cell cycle / cell division / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | ||||||
Authors | Guo, Z. / Zhan, X. / Wang, C. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Structure of a SIN3-HDAC complex from budding yeast. Authors: Zhouyan Guo / Chen Chu / Yichen Lu / Xiaofeng Zhang / Yihang Xiao / Mingxuan Wu / Shuaixin Gao / Catherine C L Wong / Xiechao Zhan / Chengcheng Wang / Abstract: SIN3-HDAC (histone deacetylases) complexes have important roles in facilitating local histone deacetylation to regulate chromatin accessibility and gene expression. Here, we present the cryo-EM ...SIN3-HDAC (histone deacetylases) complexes have important roles in facilitating local histone deacetylation to regulate chromatin accessibility and gene expression. Here, we present the cryo-EM structure of the budding yeast SIN3-HDAC complex Rpd3L at an average resolution of 2.6 Å. The structure reveals that two distinct arms (ARM1 and ARM2) hang on a T-shaped scaffold formed by two coiled-coil domains. In each arm, Sin3 interacts with different subunits to create a different environment for the histone deacetylase Rpd3. ARM1 is in the inhibited state with the active site of Rpd3 blocked, whereas ARM2 is in an open conformation with the active site of Rpd3 exposed to the exterior space. The observed asymmetric architecture of Rpd3L is different from those of available structures of other class I HDAC complexes. Our study reveals the organization mechanism of the SIN3-HDAC complex and provides insights into the interaction pattern by which it targets histone deacetylase to chromatin. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hpo.cif.gz | 680.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hpo.ent.gz | 521.1 KB | Display | PDB format |
PDBx/mmJSON format | 8hpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/8hpo ftp://data.pdbj.org/pub/pdb/validation_reports/hp/8hpo | HTTPS FTP |
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-Related structure data
Related structure data | 34935MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Transcriptional regulatory protein ... , 8 types, 9 molecules KDIABHCEJ
#1: Protein | Mass: 51075.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: Q03010 | ||||||||
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#2: Protein | Mass: 37765.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P40505 | ||||||||
#5: Protein | Mass: 23144.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P38429 | ||||||||
#6: Protein | Mass: 175047.266 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P22579 #7: Protein | | Mass: 47035.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P31385 #8: Protein | | Mass: 37081.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P50947 #9: Protein | | Mass: 48844.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P38255 #10: Protein | | Mass: 33851.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: Q07458 |
-Histone deacetylase ... , 2 types, 2 molecules FG
#3: Protein | Mass: 49361.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P32561, histone deacetylase |
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#4: Protein | Mass: 48961.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P32561, histone deacetylase |
-Non-polymers , 3 types, 7 molecules
#11: Chemical | ChemComp-TPO / | ||
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#12: Chemical | #13: Chemical | ChemComp-K / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: The Rpd3L complex / Type: COMPLEX / Entity ID: #1-#10 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2300 nm / Nominal defocus min: 1800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 665105 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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