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- PDB-9v2v: Cryo-EM structure of the histone deacetylase complex Rpd3L in com... -

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Basic information

Entry
Database: PDB / ID: 9v2v
TitleCryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome
Components
  • (DNA (155-MER)) x 2
  • (Histone deacetylase ...) x 2
  • (Transcriptional regulatory protein ...) x 7
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
KeywordsGENE REGULATION/DNA / Histone deacetylase complex / Histone modification / Rpd3L / Cryo-EM / mono-nucleosome / GENE REGULATION-DNA complex
Function / homology
Function and homology information


negative regulation of phosphatidylserine biosynthetic process / negative regulation of inositol biosynthetic process / positive regulation of phosphatidylserine biosynthetic process / positive regulation of inositol biosynthetic process / negative regulation of phosphatidylcholine biosynthetic process / regulation of invasive growth in response to glucose limitation / conjugation with cellular fusion / PI5P Regulates TP53 Acetylation / 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 / positive regulation of inositol biosynthetic process / negative regulation of phosphatidylcholine biosynthetic process / regulation of invasive growth in response to glucose limitation / conjugation with cellular fusion / PI5P Regulates TP53 Acetylation / positive regulation of phosphatidylcholine biosynthetic process / Snt2C complex / negative regulation of silent mating-type cassette heterochromatin formation / positive regulation of invasive growth in response to glucose limitation / Rpd3L complex / protein localization to nucleolar rDNA repeats / negative regulation of reciprocal meiotic recombination / negative regulation of rDNA heterochromatin formation / Rpd3L-Expanded complex / invasive growth in response to glucose limitation / Rpd3S complex / rDNA chromatin condensation / nucleophagy / SUMOylation of transcription cofactors / HDACs deacetylate histones / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / cell adhesion involved in single-species biofilm formation / histone H3K4me3 reader activity / histone deacetylase activity / negative regulation of transcription by RNA polymerase I / SUMOylation of chromatin organization proteins / cellular response to nitrogen starvation / regulation of DNA-templated DNA replication initiation / Sin3-type complex / histone deacetylase complex / Estrogen-dependent gene expression / positive regulation of macroautophagy / Ub-specific processing proteases / nuclear periphery / meiotic cell cycle / transcription coregulator activity / 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 / histone deacetylase binding / structural constituent of chromatin / transcription corepressor activity / nucleosome / heterochromatin formation / nucleosome assembly / cellular response to heat / chromatin organization / response to oxidative stress / transcription coactivator activity / protein heterodimerization activity / cell division / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Histone deacetylation protein Rxt3 / Histone deacetylation protein Rxt3 / Transcriptional regulatory protein RXT2, N-terminal / Transcriptional regulatory protein Rxt2 / RXT2-like, N-terminal / 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 ...: / Histone deacetylation protein Rxt3 / Histone deacetylation protein Rxt3 / Transcriptional regulatory protein RXT2, N-terminal / Transcriptional regulatory protein Rxt2 / RXT2-like, N-terminal / 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 / PhD finger domain / 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 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 / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / 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
DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Histone H2B / Transcriptional regulatory protein SIN3 / Transcriptional regulatory protein DEP1 / Histone deacetylase RPD3 / Transcriptional regulatory protein RXT2 / Transcriptional regulatory protein SAP30 ...DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Histone H2B / 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 / Histone H4 / Transcriptional regulatory protein RXT3 / Histone deacetylase complex subunit CTI6 / Histone H2A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Xenopus laevis (African clawed frog)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsZhao, H. / Li, H. / Wang, C. / Yang, X. / Li, H. / Zou, B. / Dong, S. / Zhang, N. / Zhou, Y. / Yi, L. ...Zhao, H. / Li, H. / Wang, C. / Yang, X. / Li, H. / Zou, B. / Dong, S. / Zhang, N. / Zhou, Y. / Yi, L. / Zhang, Y. / Xie, Y. / Qin, D. / Chao, W. / Pei, D. / He, J.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32361163669 China
National Natural Science Foundation of China (NSFC)32170189 China
National Natural Science Foundation of China (NSFC)32241021 China
Other government2023B1212060050
Other government2023B1212120009
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Chromatin context-dependent deacetylation by the asymmetric Rpd3L.
Authors: Heyu Zhao / Huadong Li / Chi Wang / Xuechen Yang / Binqian Zou / Shuqi Dong / Nan Zhang / Yuxing Zhou / Li Yi / Ying Zhang / Yixuan Xie / Dajiang Qin / William Chong Hang Chao / Duanqing Pei / Jun He /
Abstract: The regulation of gene expression requires precise control of chromatin-associated complexes that respond to diverse structural and epigenetic cues. The Rpd3 Large (Rpd3L) complex is a Sin3 histone ...The regulation of gene expression requires precise control of chromatin-associated complexes that respond to diverse structural and epigenetic cues. The Rpd3 Large (Rpd3L) complex is a Sin3 histone deacetylase complex (HDAC) that dynamically adapt to chromatin states to reinforce transcriptional silencing, yet the mechanisms governing the catalytic activation in chromatin context-dependent manner remain unclear. Here we present the cryo-electron microscopy structure of Rpd3L bound to both mono- and di-nucleosome substrate at near-atomic resolution, uncovering a substrate-guided allosteric activation mechanism. Rpd3L adopts an asymmetric architecture, in which the proximal catalytic module anchors the first nucleosome, while the Sin3 PAH domains engage linker DNA to reposition a second nucleosome. This spatial configuration brings the distal catalytic module into proximity with chromatin and unlocks its latent deacetylase activity. Biochemical and mass spectrometry analyses confirm that dual nucleosome engagement selectively enhances Rpd3L activity and broadens substrate specificity. Together, these findings establish a hierarchical mechanism by which Rpd3L interprets histone modifications and nucleosome organization to modulate its enzymatic output at promoter regions. Our study provides a framework for understanding higher-order chromatin repression mechanisms by chromatin-regulation complexes and co-repressors.
History
DepositionMay 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
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Revision 2.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulatory protein SIN3
B: Transcriptional regulatory protein SIN3
C: Histone deacetylase RPD3
D: Histone deacetylase RPD3
E: Transcriptional regulatory protein DEP1
F: Transcriptional regulatory protein SDS3
G: Transcriptional regulatory protein SAP30
H: Transcriptional regulatory protein RXT3
I: Transcriptional regulatory protein PHO23
J: Transcriptional regulatory protein RXT2
K: Histone deacetylase complex subunit CTI6
O: Histone H2A
P: Histone H2B
Q: Histone H3
R: Histone H4
S: Histone H2A
T: Histone H2B
U: Histone H3
V: Histone H4
X: DNA (155-MER)
Y: DNA (155-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)584,44222
Polymers584,37721
Non-polymers651
Water00
1


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

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Components

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

#1: Protein Transcriptional regulatory protein SIN3


Mass: 80758.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SIN3, CPE1, GAM2, RPD1, SDI1, SDS16, UME4, YOL004W / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P22579
#3: Protein Transcriptional regulatory protein DEP1


Mass: 14553.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: DEP1, FUN54, YAL013W / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P31385
#4: Protein Transcriptional regulatory protein SDS3 / Suppressor of defective silencing protein 3


Mass: 35851.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SDS3, YIL084C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P40505
#5: Protein Transcriptional regulatory protein SAP30


Mass: 14480.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SAP30, YMR263W, YM8156.05 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P38429
#6: Protein Transcriptional regulatory protein RXT3


Mass: 23933.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RXT3, YDL076C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q07458
#7: Protein Transcriptional regulatory protein PHO23


Mass: 12360.187 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: PHO23, YNL097C, N2205 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P50947
#8: Protein Transcriptional regulatory protein RXT2


Mass: 24683.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RXT2, RAF60, YBR095C, YBR0822 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P38255

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Histone deacetylase ... , 2 types, 3 molecules CDK

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


Mass: 43524.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPD3, MOF6, REC3, SDI2, SDS6, YNL330C, N0305 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32561, histone deacetylase
#9: Protein Histone deacetylase complex subunit CTI6 / CYC8-TUP1-interacting protein 6 / Transcriptional regulatory protein CTI6


Mass: 28742.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: CTI6, RXT1, YPL181W / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q08923

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Protein , 4 types, 8 molecules OSPTQURV

#10: Protein Histone H2A


Mass: 11722.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8
#11: Protein Histone H2B


Mass: 10406.954 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC108704302 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8J1LZU9
#12: Protein Histone H3


Mass: 11560.538 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC121398065, LOC108703785, LOC121398067 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1
#13: Protein Histone H4


Mass: 9066.641 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

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DNA chain , 2 types, 2 molecules XY

#14: DNA chain DNA (155-MER)


Mass: 48115.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#15: DNA chain DNA (155-MER)


Mass: 47577.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 1 types, 1 molecules

#16: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome
Type: COMPLEX / Entity ID: #1, #3-#15 / Source: MULTIPLE SOURCES
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 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

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 451544 / Symmetry type: POINT

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