+Open data
-Basic information
Entry | Database: PDB / ID: 8i02 | ||||||
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Title | Cryo-EM structure of the SIN3S complex from S. pombe | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / SIN3 / SIN3S / Pst2 / Clr6 / deacetylase | ||||||
Function / homology | Function and homology information histone H3K9 deacetylase activity / histone H3K14 deacetylase activity / histone H4K16 deacetylase activity / : / HDACs deacetylate histones / H3-H4 histone complex chaperone activity / SUMOylation of chromatin organization proteins / Rpd3S complex / Rpd3L complex / Rpd3L-Expanded complex ...histone H3K9 deacetylase activity / histone H3K14 deacetylase activity / histone H4K16 deacetylase activity / : / HDACs deacetylate histones / H3-H4 histone complex chaperone activity / SUMOylation of chromatin organization proteins / Rpd3S complex / Rpd3L complex / Rpd3L-Expanded complex / NuRD complex / histone deacetylase / protein lysine deacetylase activity / DNA repair-dependent chromatin remodeling / histone deacetylase activity / Sin3-type complex / NuA4 histone acetyltransferase complex / epigenetic regulation of gene expression / nucleosome binding / transcription initiation-coupled chromatin remodeling / mitotic spindle / transcription corepressor activity / histone binding / chromatin remodeling / DNA repair / DNA damage response / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Wang, C. / Guo, Z. / Zhan, X. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Discov / Year: 2023 Title: Two assembly modes for SIN3 histone deacetylase complexes. Authors: Chengcheng Wang / Zhouyan Guo / Chen Chu / Yichen Lu / Xiaofeng Zhang / Xiechao Zhan / Abstract: The switch-independent 3 (SIN3)/histone deacetylase (HDAC) complexes play essential roles in regulating chromatin accessibility and gene expression. There are two major types of SIN3/HDAC complexes ...The switch-independent 3 (SIN3)/histone deacetylase (HDAC) complexes play essential roles in regulating chromatin accessibility and gene expression. There are two major types of SIN3/HDAC complexes (named SIN3L and SIN3S) targeting different chromatin regions. Here we present the cryo-electron microscopy structures of the SIN3L and SIN3S complexes from Schizosaccharomyces pombe (S. pombe), revealing two distinct assembly modes. In the structure of SIN3L, each Sin3 isoform (Pst1 and Pst3) interacts with one histone deacetylase Clr6, and one WD40-containing protein Prw1, forming two lobes. These two lobes are bridged by two vertical coiled-coil domains from Sds3/Dep1 and Rxt2/Png2, respectively. In the structure of SIN3S, there is only one lobe organized by another Sin3 isoform Pst2; each of the Cph1 and Cph2 binds to an Eaf3 molecule, providing two modules for histone recognition and binding. Notably, the Pst1 Lobe in SIN3L and the Pst2 Lobe in SIN3S adopt similar conformation with their deacetylase active sites exposed to the space; however, the Pst3 Lobe in SIN3L is in a compact state with its active center buried inside and blocked. Our work reveals two classical organization mechanisms for the SIN3/HDAC complexes to achieve specific targeting and provides a framework for studying the histone deacetylase complexes. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i02.cif.gz | 471.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i02.ent.gz | 365.4 KB | Display | PDB format |
PDBx/mmJSON format | 8i02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i02_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8i02_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8i02_validation.xml.gz | 79 KB | Display | |
Data in CIF | 8i02_validation.cif.gz | 118.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/8i02 ftp://data.pdbj.org/pub/pdb/validation_reports/i0/8i02 | HTTPS FTP |
-Related structure data
Related structure data | 35092MC 8i03C 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
-Protein , 6 types, 7 molecules FABCDEG
#1: Protein | Mass: 45046.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q09819 | ||
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#2: Protein | Mass: 125011.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O13919 | ||
#3: Protein | Mass: 46165.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O59702, histone deacetylase | ||
#4: Protein | Mass: 48528.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14021 | ||
#5: Protein | Mass: 39191.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O13953 #6: Protein | | Mass: 68871.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q09698 |
-Non-polymers , 2 types, 8 molecules
#7: Chemical | ChemComp-ZN / #8: Chemical | |
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-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 SIN3S complex / Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL |
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Source (natural) | Organism: Schizosaccharomyces pombe (fission 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 FIELD / 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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 777199 / Symmetry type: POINT | ||||||||||||||||||||||||
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