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- PDB-8ga8: Structure of the yeast (HDAC) Rpd3L complex -

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Basic information

Entry
Database: PDB / ID: 8ga8
TitleStructure of the yeast (HDAC) Rpd3L complex
Components
  • (Transcriptional regulatory protein ...) x 7
  • Histone deacetylase RPD3
KeywordsTRANSCRIPTION / HDAC / Silencing / chromatin
Function / homology
Function and homology information


negative regulation of phosphatidylserine biosynthetic process / negative regulation of inositol 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 phosphatidylserine biosynthetic process / negative regulation of inositol 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 silent mating-type cassette heterochromatin formation / negative regulation of reciprocal meiotic recombination / positive regulation of invasive growth in response to glucose limitation / Rpd3L complex / protein localization to nucleolar rDNA repeats / invasive growth in response to glucose limitation / negative regulation of rDNA heterochromatin formation / Rpd3L-Expanded complex / Rpd3S complex / rDNA chromatin condensation / SUMOylation of transcription cofactors / nucleophagy / HDACs deacetylate histones / histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K4 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / histone H4K12 deacetylase activity, hydrolytic mechanism / histone deacetylase / histone H3K9 deacetylase activity, hydrolytic mechanism / cell adhesion involved in single-species biofilm formation / SUMOylation of chromatin organization proteins / cellular response to nitrogen starvation / regulation of DNA-templated DNA replication initiation / negative regulation of transcription by RNA polymerase I / histone deacetylase activity / Sin3-type complex / Estrogen-dependent gene expression / positive regulation of macroautophagy / histone deacetylase complex / Ub-specific processing proteases / : / nuclear periphery / meiotic cell cycle / transcription coregulator activity / transcription elongation by RNA polymerase II / double-strand break repair via nonhomologous end joining / G1/S transition of mitotic cell cycle / histone deacetylase binding / transcription corepressor activity / G2/M transition of mitotic cell cycle / heterochromatin formation / nucleosome assembly / chromatin organization / cellular response to heat / response to oxidative stress / transcription coactivator activity / cell division / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Transcriptional regulatory protein RXT2, N-terminal / Histone deacetylation protein Rxt3 / Transcriptional regulatory protein Rxt2 / RXT2-like, N-terminal / Histone deacetylation protein Rxt3 / Histone deacetylase complex subunit SAP30/SAP30-like / Histone deacetylase complex subunit SAP30, Sin3 binding domain / SAP30, C-terminal domain superfamily / Sin3 binding region of histone deacetylase complex subunit SAP30 / Sds3-like ...Transcriptional regulatory protein RXT2, N-terminal / Histone deacetylation protein Rxt3 / Transcriptional regulatory protein Rxt2 / RXT2-like, N-terminal / Histone deacetylation protein Rxt3 / Histone deacetylase complex subunit SAP30/SAP30-like / Histone deacetylase complex subunit SAP30, Sin3 binding domain / SAP30, C-terminal domain superfamily / Sin3 binding region of histone deacetylase complex subunit SAP30 / Sds3-like / Sds3-like / Sds3-like / Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / ING family / Histone deacetylase interacting domain / Sin3, C-terminal / Transcriptional regulatory protein Sin3-like / Sin3 family co-repressor / C-terminal domain of Sin3a protein / Histone deacetylase (HDAC) interacting / Paired amphipathic helix / Paired amphipathic helix superfamily / Paired amphipathic helix repeat / PAH domain profile. / Histone deacetylase / Histone deacetylase domain / Arginase; Chain A / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulatory protein SIN3 / Transcriptional regulatory protein DEP1 / Histone deacetylase RPD3 / Transcriptional regulatory protein RXT2 / Transcriptional regulatory protein SAP30 / Transcriptional regulatory protein SDS3 / Transcriptional regulatory protein PHO23 / Transcriptional regulatory protein RXT3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsPatel, A.B. / Radhakrishnan, I. / He, Y.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM135651 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM144559 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01CA092584 United States
American Heart Association17GRNT33680167 United States
CitationJournal: 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
DepositionFeb 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
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Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2May 14, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1May 14, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Transcriptional regulatory protein SDS3
A: Transcriptional regulatory protein SIN3
J: Transcriptional regulatory protein SAP30
L: Transcriptional regulatory protein PHO23
M: Transcriptional regulatory protein RXT2
G: Transcriptional regulatory protein DEP1
B: Histone deacetylase RPD3
E: Histone deacetylase RPD3
K: Transcriptional regulatory protein RXT3
D: Transcriptional regulatory protein SIN3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)675,55212
Polymers675,42110
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Transcriptional regulatory protein ... , 7 types, 8 molecules HADJLMGK

#1: Protein Transcriptional regulatory protein SDS3 / Suppressor of defective silencing protein 3


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
#2: Protein Transcriptional regulatory protein SIN3


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 Transcriptional regulatory protein SAP30


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 Transcriptional regulatory protein PHO23


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 Transcriptional regulatory protein RXT2


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 Transcriptional regulatory protein DEP1


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 Transcriptional regulatory protein RXT3


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

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Protein / Non-polymers , 2 types, 4 molecules BE

#7: Protein Histone deacetylase RPD3 / Transcriptional regulatory protein RPD3


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 ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Rpd3L / Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameCategory
2SerialEMimage acquisition
8PHENIXmodel refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 210993 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00322481
ELECTRON MICROSCOPYf_angle_d0.52830317
ELECTRON MICROSCOPYf_dihedral_angle_d3.6042943
ELECTRON MICROSCOPYf_chiral_restr0.0383282
ELECTRON MICROSCOPYf_plane_restr0.0043894

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