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- PDB-7yi1: Cryo-EM structure of Eaf3 CHD bound to H3K36me3 nucleosome -

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Basic information

Entry
Database: PDB / ID: 7yi1
TitleCryo-EM structure of Eaf3 CHD bound to H3K36me3 nucleosome
Components
  • (Wisdom 601 DNA (167- ...) x 2
  • Chromatin modification-related protein EAF3
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3
  • Histone H4
KeywordsGENE REGULATION / Dynamic Histone Modifications / Histone Deacetylase Complex
Function / homology
Function and homology information


nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Rpd3S complex / regulation of RNA stability / DNA replication-dependent chromatin assembly / nucleosome disassembly / regulation of DNA-templated DNA replication initiation / NuA4 histone acetyltransferase complex / histone acetyltransferase complex / transcription elongation by RNA polymerase II ...nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Rpd3S complex / regulation of RNA stability / DNA replication-dependent chromatin assembly / nucleosome disassembly / regulation of DNA-templated DNA replication initiation / NuA4 histone acetyltransferase complex / histone acetyltransferase complex / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA repair / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
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 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily ...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 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Histone H2B 1.1 / Histone H4 / Chromatin modification-related protein EAF3 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
synthetic construct (others)
Saccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLi, H.T. / Yan, C.Y. / Guan, H.P. / Wang, P.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31725014 China
National Natural Science Foundation of China (NSFC)91753203 China
Ministry of Science and Technology (MoST, China)2020YFA0803300 China
Ministry of Science and Technology (MoST, China)2021YFA1300100 China
CitationJournal: Nature / Year: 2023
Title: Diverse modes of H3K36me3-guided nucleosomal deacetylation by Rpd3S.
Authors: Haipeng Guan / Pei Wang / Pei Zhang / Chun Ruan / Yutian Ou / Bo Peng / Xiangdong Zheng / Jianlin Lei / Bing Li / Chuangye Yan / Haitao Li /
Abstract: Context-dependent dynamic histone modifications constitute a key epigenetic mechanism in gene regulation. The Rpd3 small (Rpd3S) complex recognizes histone H3 trimethylation on lysine 36 (H3K36me3) ...Context-dependent dynamic histone modifications constitute a key epigenetic mechanism in gene regulation. The Rpd3 small (Rpd3S) complex recognizes histone H3 trimethylation on lysine 36 (H3K36me3) and deacetylates histones H3 and H4 at multiple sites across transcribed regions. Here we solved the cryo-electron microscopy structures of Saccharomyces cerevisiae Rpd3S in its free and H3K36me3 nucleosome-bound states. We demonstrated a unique architecture of Rpd3S, in which two copies of Eaf3-Rco1 heterodimers are asymmetrically assembled with Rpd3 and Sin3 to form a catalytic core complex. Multivalent recognition of two H3K36me3 marks, nucleosomal DNA and linker DNAs by Eaf3, Sin3 and Rco1 positions the catalytic centre of Rpd3 next to the histone H4 N-terminal tail for deacetylation. In an alternative catalytic mode, combinatorial readout of unmethylated histone H3 lysine 4 and H3K36me3 by Rco1 and Eaf3 directs histone H3-specific deacetylation except for the registered histone H3 acetylated lysine 9. Collectively, our work illustrates dynamic and diverse modes of multivalent nucleosomal engagement and methylation-guided deacetylation by Rpd3S, highlighting the exquisite complexity of epigenetic regulation with delicately designed multi-subunit enzymatic machineries in transcription and beyond.
History
DepositionJul 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: Wisdom 601 DNA (167-MER)
J: Wisdom 601 DNA (167-MER)
K: Chromatin modification-related protein EAF3
L: Chromatin modification-related protein EAF3
A: Histone H3
E: Histone H3


Theoretical massNumber of molelcules
Total (without water)301,86412
Polymers301,86412
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 10 molecules BFCGDHKLAE

#1: 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
#2: 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8
#3: 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
#6: 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 S288C (yeast) / Strain: S288c / Gene: EAF3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q12432
#7: Protein Histone H3 /


Mass: 15346.010 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog)
Gene: LOC108703785, LOC121398065, LOC121398067, XELAEV_18002543mg
Production host: synthetic construct (others) / References: UniProt: A0A310TTQ1

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Wisdom 601 DNA (167- ... , 2 types, 2 molecules IJ

#4: DNA chain Wisdom 601 DNA (167-MER)


Mass: 51308.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#5: DNA chain Wisdom 601 DNA (167-MER)


Mass: 51798.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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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: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Rpd3S complex with H3K36me3 nucleosomeCOMPLEXall0RECOMBINANT
2Histone H4/H2A/H2B 1.1COMPLEX#1-#31RECOMBINANT
3DNACOMPLEX#4-#51RECOMBINANT
4EAF3COMPLEX#61RECOMBINANT
5Histone H3COMPLEX#71RECOMBINANT
Molecular weightValue: 723 kDa/nm / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Xenopus laevis (African clawed frog)8355
32synthetic construct (others)32630
43Saccharomyces cerevisiae S288C (yeast)559292
54Xenopus laevis (African clawed frog)8355
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
32synthetic construct (others)32630
43Spodoptera frugiperda (fall armyworm)7108
54synthetic construct (others)32630
Buffer solutionpH: 7.5
SpecimenConc.: 0.7 mg/ml / Embedding 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: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1800 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 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: 1.20.1_4487: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 427166 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314803
ELECTRON MICROSCOPYf_angle_d0.55921278
ELECTRON MICROSCOPYf_dihedral_angle_d30.3634110
ELECTRON MICROSCOPYf_chiral_restr0.0342388
ELECTRON MICROSCOPYf_plane_restr0.0051642

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