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Open data
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Basic information
Entry | Database: PDB / ID: 8ihn | ||||||
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Title | Cryo-EM structure of the Rpd3S core complex | ||||||
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![]() | TRANSCRIPTION / HDAC | ||||||
Function / homology | ![]() Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / protein localization to nucleolar rDNA repeats / negative regulation of rDNA heterochromatin formation / Rpd3S complex / Rpd3L complex / Rpd3L-Expanded complex / rDNA chromatin condensation / nucleophagy ...Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / protein localization to nucleolar rDNA repeats / negative regulation of rDNA heterochromatin formation / Rpd3S complex / Rpd3L complex / Rpd3L-Expanded complex / rDNA chromatin condensation / nucleophagy / HDACs deacetylate histones / NuRD complex / histone deacetylase / SUMOylation of chromatin organization proteins / regulation of DNA-templated DNA replication initiation / negative regulation of transcription by RNA polymerase I / histone deacetylase activity / Sin3-type complex / NuA4 histone acetyltransferase complex / Estrogen-dependent gene expression / histone deacetylase complex / positive regulation of macroautophagy / nuclear periphery / transcription elongation by RNA polymerase II / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / response to oxidative stress / transcription coactivator activity / chromatin remodeling / cell cycle / protein heterodimerization activity / cell division / DNA repair / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å | ||||||
![]() | Zhang, Y. / Gang, C. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural basis for nucleosome binding and catalysis by the yeast Rpd3S/HDAC holoenzyme. Authors: Yueyue Zhang / Mengxue Xu / Po Wang / Jiahui Zhou / Guangxian Wang / Shuailong Han / Gang Cai / Xuejuan Wang / ![]() | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 383.7 KB | Display | ![]() |
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PDB format | ![]() | 278 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 59.4 KB | Display | |
Data in CIF | ![]() | 89.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 35450MC ![]() 8ihmC ![]() 8ihtC M: map data used to model this data C: citing same article ( |
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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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1 |
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Components
-Protein/peptide , 1 types, 1 molecules A
#1: Protein/peptide | Mass: 2563.012 Da / Num. of mol.: 1 / Fragment: N-ter Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Protein , 4 types, 6 molecules KLMONP
#2: Protein | Mass: 175047.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||
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#3: Protein | Mass: 48961.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||
#4: Protein | Mass: 78951.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 45266.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 2 types, 2 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CA.gif)
#6: Chemical | ChemComp-ZN / |
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#7: Chemical | ChemComp-CA / |
-Details
Has ligand of interest | Y |
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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 |
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Sample preparation
Component | Name: Eaf3 CHD domain bound to the nucleosome / Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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 / Nominal defocus max: 2800 nm / Nominal defocus min: 1800 nm |
Image recording | Electron dose: 53 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107252 / Symmetry type: POINT | ||||||||||||||||||||||||
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