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- PDB-8kd3: Rpd3S in complex with nucleosome with H3K36MLA modification, H3K9... -

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Basic information

Entry
Database: PDB / ID: 8kd3
TitleRpd3S in complex with nucleosome with H3K36MLA modification, H3K9Q mutation and 187bp DNA
Components
  • (187bp DNA) x 2
  • (Transcriptional regulatory protein ...) x 2
  • Chromatin modification-related protein EAF3
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3
  • Histone H4
  • Histone deacetylase RPD3
KeywordsTRANSCRIPTION / Rpd3S / HDAC / Hho1 / cryptic transcription
Function / homology
Function and homology information


nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / 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 ...nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / 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 / regulation of RNA stability / nucleophagy / HDACs deacetylate histones / DNA replication-dependent chromatin assembly / histone deacetylase / nucleosome disassembly / 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 / NuA4 histone acetyltransferase complex / Sin3-type complex / positive regulation of macroautophagy / Estrogen-dependent gene expression / histone deacetylase complex / histone acetyltransferase complex / methylated histone binding / nuclear periphery / meiotic cell cycle / positive regulation of transcription elongation by RNA polymerase II / transcription elongation by RNA polymerase II / heterochromatin formation / double-strand break repair via nonhomologous end joining / G1/S transition of mitotic cell cycle / structural constituent of chromatin / transcription corepressor activity / G2/M transition of mitotic cell cycle / nucleosome / nucleosome assembly / cellular response to heat / response to oxidative stress / transcription coactivator activity / protein heterodimerization activity / cell division / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription / 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
: / : / MSL3 chromodomain-like / 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 ...: / : / MSL3 chromodomain-like / 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. / 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. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Zinc finger, FYVE/PHD-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Histone H2B 1.1 / Transcriptional regulatory protein SIN3 / Histone deacetylase RPD3 / Histone H4 / Transcriptional regulatory protein RCO1 / Chromatin modification-related protein EAF3 / Histone H2A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Xenopus laevis (African clawed frog)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsDong, S. / Li, H. / Wang, M. / Rasheed, N. / Zou, B. / Gao, X. / Guan, J. / Li, W. / Zhang, J. / Wang, C. ...Dong, S. / Li, H. / Wang, M. / Rasheed, N. / Zou, B. / Gao, X. / Guan, J. / Li, W. / Zhang, J. / Wang, C. / Zhou, N. / Shi, X. / Li, M. / Zhou, M. / Huang, J. / Li, H. / Zhang, Y. / Wong, K.H. / Zhang, X. / Chao, W.C.H. / He, J.
Funding support China, 8items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)NSFC U20A2013 China
National Natural Science Foundation of China (NSFC)32241021 China
National Natural Science Foundation of China (NSFC)32170189 China
Other governmentMYRG2018-00221-FHS
Other government0009/2018/A1
Other government0032/2021/A1
Other government202102080156
Other government2019QN01Y051
CitationJournal: Cell Res / Year: 2023
Title: Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex.
Authors: Shuqi Dong / Huadong Li / Meilin Wang / Nadia Rasheed / Binqian Zou / Xijie Gao / Jiali Guan / Weijie Li / Jiale Zhang / Chi Wang / Ningkun Zhou / Xue Shi / Mei Li / Min Zhou / Junfeng Huang ...Authors: Shuqi Dong / Huadong Li / Meilin Wang / Nadia Rasheed / Binqian Zou / Xijie Gao / Jiali Guan / Weijie Li / Jiale Zhang / Chi Wang / Ningkun Zhou / Xue Shi / Mei Li / Min Zhou / Junfeng Huang / He Li / Ying Zhang / Koon Ho Wong / Xiaofei Zhang / William Chong Hang Chao / Jun He /
Abstract: In Saccharomyces cerevisiae, cryptic transcription at the coding region is prevented by the activity of Sin3 histone deacetylase (HDAC) complex Rpd3S, which is carried by the transcribing RNA ...In Saccharomyces cerevisiae, cryptic transcription at the coding region is prevented by the activity of Sin3 histone deacetylase (HDAC) complex Rpd3S, which is carried by the transcribing RNA polymerase II (RNAPII) to deacetylate and stabilize chromatin. Despite its fundamental importance, the mechanisms by which Rpd3S deacetylates nucleosomes and regulates chromatin dynamics remain elusive. Here, we determined several cryo-EM structures of Rpd3S in complex with nucleosome core particles (NCPs), including the H3/H4 deacetylation states, the alternative deacetylation state, the linker tightening state, and a state in which Rpd3S co-exists with the Hho1 linker histone on NCP. These structures suggest that Rpd3S utilizes a conserved Sin3 basic surface to navigate through the nucleosomal DNA, guided by its interactions with H3K36 methylation and the extra-nucleosomal DNA linkers, to target acetylated H3K9 and sample other histone tails. Furthermore, our structures illustrate that Rpd3S reconfigures the DNA linkers and acts in concert with Hho1 to engage the NCP, potentially unraveling how Rpd3S and Hho1 work in tandem for gene silencing.
History
DepositionAug 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase RPD3
B: Transcriptional regulatory protein SIN3
D: Chromatin modification-related protein EAF3
E: Transcriptional regulatory protein RCO1
F: Chromatin modification-related protein EAF3
G: Transcriptional regulatory protein RCO1
O: Histone H3
P: Histone H4
Q: Histone H2A
R: Histone H2B 1.1
S: Histone H3
T: Histone H4
U: Histone H2A
V: Histone H2B 1.1
X: 187bp DNA
Y: 187bp DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)708,28517
Polymers708,22016
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 11 molecules ADFOSPTQURV

#1: Protein Histone deacetylase 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 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32561
#3: Protein Chromatin modification-related protein EAF3 / ESA1-associated factor 3


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: Q12432
#5: Protein Histone H3


Mass: 15312.893 Da / Num. of mol.: 2 / Mutation: C110A, K9Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC121398065 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1
#6: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#7: Protein Histone H2A


Mass: 13978.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591, XELAEV_18003602mg / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8
#8: Protein Histone H2B 1.1 / H2B1.1


Mass: 13524.752 Da / Num. of mol.: 2 / Mutation: S29T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281

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

#2: Protein Transcriptional regulatory protein SIN3


Mass: 176152.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SIN3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P22579
#4: Protein Transcriptional regulatory protein RCO1


Mass: 84469.328 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: Q04779

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DNA chain , 2 types, 2 molecules XY

#9: DNA chain 187bp DNA


Mass: 58077.926 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#10: DNA chain 187bp DNA


Mass: 57397.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 1 types, 1 molecules

#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1H3K9 deacetylation state of Rpd3S-NCP (187bp/MLA/K9Q)COMPLEX#1-#100MULTIPLE SOURCES
2Rpd3-Sin3-Eaf3-Rco1COMPLEX#1-#41RECOMBINANT
3histoneCOMPLEX#5-#81RECOMBINANT
4DNACOMPLEX#9-#101SYNTHETIC
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Saccharomyces cerevisiae (brewer's yeast)4932
33Xenopus laevis (African clawed frog)8355
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Trichoplusia ni (cabbage looper)7111
33Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
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 FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 117400 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00428818
ELECTRON MICROSCOPYf_angle_d0.75640309
ELECTRON MICROSCOPYf_dihedral_angle_d26.536127
ELECTRON MICROSCOPYf_chiral_restr0.0424439
ELECTRON MICROSCOPYf_plane_restr0.0063999

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