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- PDB-8w9e: Cryo-EM structure of the Rpd3S-nucleosome complex from budding ye... -

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Basic information

Entry
Database: PDB / ID: 8w9e
TitleCryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2
Components
  • (Transcriptional regulatory protein ...) x 2
  • 3-DNA
  • 5-DNA
  • Chromatin modification-related protein EAF3
  • Histone H2A type 1-B/E
  • Histone H2B type 1-K
  • Histone H3.1Histone H3
  • Histone H4
  • Histone deacetylase RPD3
KeywordsDNA BINDING PROTEIN/DNA / Rpd3S / HDAC / Sin3 / Rpd3 / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / Rpd3L complex / protein localization to nucleolar rDNA repeats / Rpd3S complex / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation ...nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / Rpd3L complex / protein localization to nucleolar rDNA repeats / Rpd3S complex / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / HDACs deacetylate histones / regulation of RNA stability / rDNA chromatin condensation / nucleophagy / DNA replication-dependent chromatin assembly / SUMOylation of chromatin organization proteins / nucleosome disassembly / histone deacetylase / regulation of DNA-templated DNA replication initiation / negative regulation of transcription by RNA polymerase I / histone deacetylase activity / NuA4 histone acetyltransferase complex / Sin3-type complex / heterochromatin organization / histone deacetylase complex / positive regulation of macroautophagy / nucleosomal DNA binding / histone acetyltransferase complex / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / epigenetic regulation of gene expression / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / nuclear periphery / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / transcription elongation by RNA polymerase II / RNA Polymerase I Promoter Escape / positive regulation of transcription elongation by RNA polymerase II / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / HDMs demethylate histones / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / double-strand break repair via nonhomologous end joining / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / transcription corepressor activity / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / gene expression / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Processing of DNA double-strand break ends / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / killing of cells of another organism / Estrogen-dependent gene expression / response to oxidative stress
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. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA (> 100) / Histone H2B type 1-K / Histone H2A type 1-B/E / Transcriptional regulatory protein SIN3 / Histone deacetylase RPD3 / Histone H4 / Histone H3.1 ...: / DNA / DNA (> 10) / DNA (> 100) / Histone H2B type 1-K / Histone H2A type 1-B/E / Transcriptional regulatory protein SIN3 / Histone deacetylase RPD3 / Histone H4 / Histone H3.1 / Transcriptional regulatory protein RCO1 / Chromatin modification-related protein EAF3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWang, C. / Zhan, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci Adv / Year: 2024
Title: Structures and dynamics of Rpd3S complex bound to nucleosome.
Authors: Chengcheng Wang / Chen Chu / Zhouyan Guo / Xiechao Zhan /
Abstract: The Rpd3S complex plays a pivotal role in facilitating local histone deacetylation in the transcribed regions to suppress intragenic transcription initiation. Here, we present the cryo-electron ...The Rpd3S complex plays a pivotal role in facilitating local histone deacetylation in the transcribed regions to suppress intragenic transcription initiation. Here, we present the cryo-electron microscopy structures of the budding yeast Rpd3S complex in both its apo and three nucleosome-bound states at atomic resolutions, revealing the exquisite architecture of Rpd3S to well accommodate a mononucleosome without linker DNA. The Rpd3S core, containing a Sin3 Lobe and two NB modules, is a rigid complex and provides three positive-charged anchors (Sin3_HCR and two Rco1_NIDs) to connect nucleosomal DNA. In three nucleosome-bound states, the Rpd3S core exhibits three distinct orientations relative to the nucleosome, assisting the sector-shaped deacetylase Rpd3 to locate above the SHL5-6, SHL0-1, or SHL2-3, respectively. Our work provides a structural framework that reveals a dynamic working model for the Rpd3S complex to engage diverse deacetylation sites.
History
DepositionSep 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulatory protein SIN3
E: Transcriptional regulatory protein RCO1
B: Histone deacetylase RPD3
C: Chromatin modification-related protein EAF3
D: Chromatin modification-related protein EAF3
F: Transcriptional regulatory protein RCO1
a: Histone H3.1
b: Histone H4
c: Histone H2A type 1-B/E
d: Histone H2B type 1-K
e: Histone H3.1
f: Histone H4
g: Histone H2A type 1-B/E
h: Histone H2B type 1-K
i: 5-DNA
j: 3-DNA
G: Chromatin modification-related protein EAF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)718,77225
Polymers718,27517
Non-polymers4978
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Transcriptional regulatory protein ... , 2 types, 3 molecules AEF

#1: Protein Transcriptional regulatory protein SIN3


Mass: 175047.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22579
#2: Protein Transcriptional regulatory protein RCO1


Mass: 78951.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04779

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Protein , 6 types, 12 molecules BCDGaebfcgdh

#3: Protein Histone deacetylase RPD3


Mass: 48961.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32561
#4: Protein Chromatin modification-related protein EAF3 / ESA1-associated factor 3


Mass: 45266.406 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12432
#5: Protein Histone H3.1 / Histone H3


Mass: 15437.167 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68431
#6: Protein Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62805
#7: Protein Histone H2A type 1-B/E


Mass: 14165.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P04908
#8: Protein Histone H2B type 1-K


Mass: 13921.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60814

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DNA chain , 2 types, 2 molecules ij

#9: DNA chain 5-DNA


Mass: 45368.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#10: DNA chain 3-DNA


Mass: 45359.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Non-polymers , 2 types, 8 molecules

#11: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#12: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K

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Details

Has ligand of interestN

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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: The Rpd3S complex / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELDBright-field microscopy / Nominal defocus max: 2300 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 327408 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01515383
ELECTRON MICROSCOPYf_angle_d0.78420761
ELECTRON MICROSCOPYf_dihedral_angle_d11.7421994
ELECTRON MICROSCOPYf_chiral_restr0.0462242
ELECTRON MICROSCOPYf_plane_restr0.0052655

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