+Open data
-Basic information
Entry | Database: PDB / ID: 8ga8 | |||||||||||||||
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Title | Structure of the yeast (HDAC) Rpd3L complex | |||||||||||||||
Components |
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Keywords | TRANSCRIPTION / HDAC / Silencing / chromatin | |||||||||||||||
Function / homology | Function and homology information negative regulation of inositol biosynthetic process / negative regulation of phosphatidylserine biosynthetic process / positive regulation of phosphatidylserine biosynthetic process / negative regulation of phosphatidylcholine biosynthetic process / positive regulation of inositol biosynthetic process / regulation of invasive growth in response to glucose limitation / PI5P Regulates TP53 Acetylation / conjugation with cellular fusion / positive regulation of phosphatidylcholine biosynthetic process / Snt2C complex ...negative regulation of inositol biosynthetic process / negative regulation of phosphatidylserine biosynthetic process / positive regulation of phosphatidylserine biosynthetic process / negative regulation of phosphatidylcholine biosynthetic process / positive regulation of inositol biosynthetic process / regulation of invasive growth in response to glucose limitation / PI5P Regulates TP53 Acetylation / conjugation with cellular fusion / positive regulation of phosphatidylcholine biosynthetic process / 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 / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / Rpd3S complex / SUMOylation of transcription cofactors / rDNA chromatin condensation / nucleophagy / HDACs deacetylate histones / cell adhesion involved in single-species biofilm formation / histone deacetylase / SUMOylation of chromatin organization proteins / cellular response to nitrogen starvation / negative regulation of transcription by RNA polymerase I / regulation of DNA-templated DNA replication initiation / histone deacetylase activity / Sin3-type complex / Estrogen-dependent gene expression / histone deacetylase complex / positive regulation of macroautophagy / Ub-specific processing proteases / methylated histone binding / nuclear periphery / meiotic cell cycle / transcription elongation by RNA polymerase II / transcription coregulator activity / heterochromatin formation / histone deacetylase binding / double-strand break repair via nonhomologous end joining / G1/S transition of mitotic cell cycle / transcription corepressor activity / G2/M transition of mitotic cell cycle / nucleosome assembly / chromatin organization / cellular response to heat / response to oxidative stress / transcription coactivator activity / cell division / 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 / mitochondrion / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||
Authors | Patel, A.B. / Radhakrishnan, I. / He, Y. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Nat Commun / Year: 2023 Title: Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex. Authors: Avinash B Patel / Jinkang Qing / Kelly H Tam / Sara Zaman / Maria Luiso / Ishwar Radhakrishnan / Yuan He / Abstract: The Rpd3L histone deacetylase (HDAC) complex is an ancient 12-subunit complex conserved in a broad range of eukaryotes that performs localized deacetylation at or near sites of recruitment by DNA- ...The Rpd3L histone deacetylase (HDAC) complex is an ancient 12-subunit complex conserved in a broad range of eukaryotes that performs localized deacetylation at or near sites of recruitment by DNA-bound factors. Here we describe the cryo-EM structure of this prototypical HDAC complex that is characterized by as many as seven subunits performing scaffolding roles for the tight integration of the only catalytic subunit, Rpd3. The principal scaffolding protein, Sin3, along with Rpd3 and the histone chaperone, Ume1, are present in two copies, with each copy organized into separate lobes of an asymmetric dimeric molecular assembly. The active site of one Rpd3 is completely occluded by a leucine side chain of Rxt2, while the tips of the two lobes and the more peripherally associated subunits exhibit varying levels of flexibility and positional disorder. The structure reveals unexpected structural homology/analogy between unrelated subunits in the fungal and mammalian complexes and provides a foundation for deeper interrogations of structure, biology, and mechanism of these complexes, as well as for the discovery of HDAC complex-specific inhibitors. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ga8.cif.gz | 546.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ga8.ent.gz | 409.8 KB | Display | PDB format |
PDBx/mmJSON format | 8ga8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ga8_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8ga8_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8ga8_validation.xml.gz | 78.8 KB | Display | |
Data in CIF | 8ga8_validation.cif.gz | 116.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/8ga8 ftp://data.pdbj.org/pub/pdb/validation_reports/ga/8ga8 | HTTPS FTP |
-Related structure data
Related structure data | 29892MC 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 ... , 7 types, 8 molecules HADJLMGK
#1: Protein | Mass: 37685.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40505 | ||||||||||
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#2: Protein | Mass: 175047.266 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22579 #3: Protein | | Mass: 23064.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38429 #4: Protein | | Mass: 37081.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P50947 #5: Protein | | Mass: 48684.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38255 #6: Protein | | Mass: 47035.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P31385 #8: Protein | | Mass: 33851.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q07458 |
-Protein / Non-polymers , 2 types, 4 molecules BE
#7: Protein | Mass: 48961.957 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32561, histone deacetylase #9: Chemical | |
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-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 |
-Sample preparation
Component | Name: Rpd3L / Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 210993 / Symmetry type: POINT | ||||||||||||||||||||||||
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