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- PDB-8i03: Cryo-EM structure of the SIN3L complex from S. pombe -

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Basic information

Entry
Database: PDB / ID: 8i03
TitleCryo-EM structure of the SIN3L complex from S. pombe
Components
  • (Paired amphipathic helix protein ...) x 2
  • (Transcriptional regulatory protein ...) x 4
  • Chromatin modification-related protein png2
  • Histone deacetylase clr6
  • RbAp48-related WD40 repeat-containing protein prw1
KeywordsDNA BINDING PROTEIN / SIN3 / SIN3L / Pst1 / Pst3 / Clr6 / deacetylase
Function / homology
Function and homology information


: / : / Regulation of TP53 Activity through Acetylation / PI5P Regulates TP53 Acetylation / : / histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / SUMOylation of transcription cofactors / histone H3K9 deacetylase activity, hydrolytic mechanism ...: / : / Regulation of TP53 Activity through Acetylation / PI5P Regulates TP53 Acetylation / : / histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / SUMOylation of transcription cofactors / histone H3K9 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / HDACs deacetylate histones / histone H4K12 deacetylase activity, hydrolytic mechanism / SUMOylation of chromatin organization proteins / H3-H4 histone complex chaperone activity / cell cycle / negative regulation of silent mating-type cassette heterochromatin formation / Rpd3L complex / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / Rpd3S complex / pericentric heterochromatin formation / histone deacetylase / protein lysine deacetylase activity / histone deacetylase activity / NuA4 histone acetyltransferase complex / Sin3-type complex / histone deacetylase complex / pericentric heterochromatin / methylated histone binding / epigenetic regulation of gene expression / transcription initiation-coupled chromatin remodeling / heterochromatin formation / histone deacetylase binding / double-strand break repair via nonhomologous end joining / transcription corepressor activity / chromatin organization / histone binding / chromatin remodeling / cell division / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
LCCL domain superfamily / Transcriptional regulatory protein RXT2, N-terminal / Histone deacetylation protein Rxt3 / Transcriptional regulatory protein Rxt2 / RXT2-like, N-terminal / Histone deacetylation protein Rxt3 / Sds3-like / Sds3-like / Sds3-like / Inhibitor of growth protein, N-terminal histone-binding ...LCCL domain superfamily / Transcriptional regulatory protein RXT2, N-terminal / Histone deacetylation protein Rxt3 / Transcriptional regulatory protein Rxt2 / RXT2-like, N-terminal / Histone deacetylation protein Rxt3 / 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-binding protein RBBP4, N-terminal / : / Histone-binding protein RBBP4 or subunit C of CAF1 complex / 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 / Zinc finger, FYVE/PHD-type / G-protein beta WD-40 repeat / Zinc finger, RING/FYVE/PHD-type / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / RbAp48-related WD40 repeat-containing protein prw1 / Histone deacetylase clr6 / Chromatin modification-related protein png2 / Paired amphipathic helix protein pst3 / Transcriptional regulatory protein rxt2 / Transcriptional regulatory protein rxt3 / Paired amphipathic helix protein pst1 / Transcriptional regulatory protein dep1 / Transcriptional regulatory protein sds3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWang, C. / Guo, Z. / Zhan, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2023
Title: Two assembly modes for SIN3 histone deacetylase complexes.
Authors: Chengcheng Wang / Zhouyan Guo / Chen Chu / Yichen Lu / Xiaofeng Zhang / Xiechao Zhan /
Abstract: The switch-independent 3 (SIN3)/histone deacetylase (HDAC) complexes play essential roles in regulating chromatin accessibility and gene expression. There are two major types of SIN3/HDAC complexes ...The switch-independent 3 (SIN3)/histone deacetylase (HDAC) complexes play essential roles in regulating chromatin accessibility and gene expression. There are two major types of SIN3/HDAC complexes (named SIN3L and SIN3S) targeting different chromatin regions. Here we present the cryo-electron microscopy structures of the SIN3L and SIN3S complexes from Schizosaccharomyces pombe (S. pombe), revealing two distinct assembly modes. In the structure of SIN3L, each Sin3 isoform (Pst1 and Pst3) interacts with one histone deacetylase Clr6, and one WD40-containing protein Prw1, forming two lobes. These two lobes are bridged by two vertical coiled-coil domains from Sds3/Dep1 and Rxt2/Png2, respectively. In the structure of SIN3S, there is only one lobe organized by another Sin3 isoform Pst2; each of the Cph1 and Cph2 binds to an Eaf3 molecule, providing two modules for histone recognition and binding. Notably, the Pst1 Lobe in SIN3L and the Pst2 Lobe in SIN3S adopt similar conformation with their deacetylase active sites exposed to the space; however, the Pst3 Lobe in SIN3L is in a compact state with its active center buried inside and blocked. Our work reveals two classical organization mechanisms for the SIN3/HDAC complexes to achieve specific targeting and provides a framework for studying the histone deacetylase complexes.
History
DepositionJan 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Paired amphipathic helix protein pst1
B: Paired amphipathic helix protein pst3
C: Histone deacetylase clr6
D: Histone deacetylase clr6
E: Transcriptional regulatory protein dep1
F: Transcriptional regulatory protein rxt2
G: Transcriptional regulatory protein sds3
H: Chromatin modification-related protein png2
I: Transcriptional regulatory protein rxt3
J: RbAp48-related WD40 repeat-containing protein prw1
K: RbAp48-related WD40 repeat-containing protein prw1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)682,71517
Polymers682,42811
Non-polymers2876
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Paired amphipathic helix protein ... , 2 types, 2 molecules AB

#1: Protein Paired amphipathic helix protein pst1 / SIN3 homolog 1


Mass: 171667.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q09750
#2: Protein Paired amphipathic helix protein pst3 / SIN3 homolog 3


Mass: 133049.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74755

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Protein , 3 types, 5 molecules CDHJK

#3: Protein Histone deacetylase clr6 / Cryptic loci regulator 6


Mass: 46165.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O59702, histone deacetylase
#7: Protein Chromatin modification-related protein png2 / ING1 homolog 2


Mass: 34925.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74736
#9: Protein RbAp48-related WD40 repeat-containing protein prw1


Mass: 48528.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14021

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Transcriptional regulatory protein ... , 4 types, 4 molecules EFGI

#4: Protein Transcriptional regulatory protein dep1


Mass: 55701.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9P7M1
#5: Protein Transcriptional regulatory protein rxt2


Mass: 27429.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O94355
#6: Protein Transcriptional regulatory protein sds3 / Clr6 histone deacetylase complex I subunit Sds3


Mass: 30800.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9UTB6
#8: Protein Transcriptional regulatory protein rxt3


Mass: 39464.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O94707

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Non-polymers , 2 types, 6 molecules

#10: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#11: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / 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 SIN3S complex / Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Buffer solutionpH: 7.4
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: 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

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 389222 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0130092
ELECTRON MICROSCOPYf_angle_d0.8440747
ELECTRON MICROSCOPYf_dihedral_angle_d13.843982
ELECTRON MICROSCOPYf_chiral_restr0.0524434
ELECTRON MICROSCOPYf_plane_restr0.0055266

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