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- PDB-8hxx: Cryo-EM structure of the histone deacetylase complex Rpd3S -

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Basic information

Entry
Database: PDB / ID: 8hxx
TitleCryo-EM structure of the histone deacetylase complex Rpd3S
Components
  • Chromatin modification-related protein EAF3
  • Histone H3
  • Histone deacetylase RPD3
  • RCO1 isoform 1
  • Transcriptional regulatory protein SIN3
KeywordsGENE REGULATION / Histone deacetylase complex
Function / homology
Function and homology information


Snt2C complex / negative regulation of silent mating-type cassette heterochromatin formation / negative regulation of reciprocal meiotic recombination / Rpd3L complex / protein localization to nucleolar rDNA repeats / negative regulation of rDNA heterochromatin formation / Rpd3L-Expanded complex / Rpd3S complex / rDNA chromatin condensation / nucleophagy ...Snt2C complex / negative regulation of silent mating-type cassette heterochromatin formation / negative regulation of reciprocal meiotic recombination / Rpd3L complex / protein localization to nucleolar rDNA repeats / negative regulation of rDNA heterochromatin formation / Rpd3L-Expanded complex / Rpd3S complex / rDNA chromatin condensation / nucleophagy / HDACs deacetylate histones / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / 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 / NuA4 histone acetyltransferase complex / Estrogen-dependent gene expression / histone deacetylase complex / positive regulation of macroautophagy / nuclear periphery / meiotic cell cycle / transcription elongation by RNA polymerase II / G1/S transition of mitotic cell cycle / double-strand break repair via nonhomologous end joining / G2/M transition of mitotic cell cycle / structural constituent of chromatin / transcription corepressor activity / nucleosome / heterochromatin formation / nucleosome assembly / cellular response to heat / response to oxidative stress / transcription coactivator activity / chromatin remodeling / protein heterodimerization activity / cell division / DNA repair / 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 / DNA binding / metal ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
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 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. / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Histone deacetylase / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, PHD-type, conserved site / PHD-finger / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H3 / RCO1 isoform 1 / Chromatin modification-related protein EAF3 / Transcriptional regulatory protein SIN3 / Histone deacetylase RPD3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Xenopus laevis (African clawed frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsCui, H. / Wang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22DAA00673 China
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Structure of histone deacetylase complex Rpd3S bound to nucleosome.
Authors: Wulong Li / Hengjun Cui / Zhimin Lu / Haibo Wang /
Abstract: Crosstalk between histone modifications represents a fundamental epigenetic mechanism in gene regulation. During the transcription elongation process, the histone deacetylase complex Rpd3S is ...Crosstalk between histone modifications represents a fundamental epigenetic mechanism in gene regulation. During the transcription elongation process, the histone deacetylase complex Rpd3S is recruited to H3K36-methylated nucleosomes to suppress cryptic transcription initiation. However, how subunits of Rpd3S are assembled and coordinated to recognize nucleosomal substrates and exert their deacetylation function remains unclear. Here we report the structure of Saccharomyces cerevisiae Rpd3S deacetylase bound to H3K36me3-modified nucleosome at 3.1 Å resolution. It shows that Sin3 and Rco1 subunits orchestrate the assembly of the complex and mediate its contact with nucleosome at multiple sites, with the Sin3-DNA interface as a pivotal anchor. The PHD1 domain of Rco1 recognizes the unmodified H3K4 and places the following H3 tail toward the active site of Rpd3, while the chromodomain of Eaf3 subunit recognizes the H3K36me3 mark and contacts both nucleosomal and linker DNA. The second copy of Eaf3-Rco1 is involved in neighboring nucleosome binding. Our work unravels the structural basis of chromatin targeting and deacetylation by the Rpd3S complex.
History
DepositionJan 5, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN
Revision 1.2Oct 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Dec 27, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary / Category: em_admin / pdbx_entry_details
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
K: Transcriptional regulatory protein SIN3
L: Histone deacetylase RPD3
M: Chromatin modification-related protein EAF3
N: RCO1 isoform 1
O: Chromatin modification-related protein EAF3
P: RCO1 isoform 1
E: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)488,23414
Polymers487,7777
Non-polymers4587
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 7 molecules KLMONPE

#1: Protein Transcriptional regulatory protein SIN3


Mass: 175047.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SIN3, CPE1, GAM2, RPD1, SDI1, SDS16, UME4, YOL004W / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P22579
#2: Protein Histone deacetylase RPD3 / Transcriptional regulatory protein RPD3


Mass: 48961.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPD3, MOF6, REC3, SDI2, SDS6, YNL330C, N0305 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32561, histone deacetylase
#3: Protein Chromatin modification-related protein EAF3


Mass: 45266.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EAF3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A8H4F719
#4: Protein RCO1 isoform 1


Mass: 78951.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RCO1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A8H4BXB0
#5: Protein Histone H3


Mass: 15331.982 Da / Num. of mol.: 1 / Mutation: C110A
Source method: isolated from a genetically manipulated source
Details: Author stated that Cys110 residue of chain E was mutated to Ala due to the preparation of ML3-modified nucleosome.
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC121398065 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1

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Non-polymers , 1 types, 7 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / 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: Rpd3S histone deacetylase in complex with histone H3 tail
Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
Details: 20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 44 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4Warp1.0.7CTF correction
7UCSF ChimeraX1.5model fitting
12RELION3.1.03D reconstruction
13PHENIX1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39789 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00715195
ELECTRON MICROSCOPYf_angle_d1.03920494
ELECTRON MICROSCOPYf_dihedral_angle_d5.1211960
ELECTRON MICROSCOPYf_chiral_restr0.0542221
ELECTRON MICROSCOPYf_plane_restr0.0082616

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