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- PDB-8vnz: PRC2_AJ1-450 bound to H3K36me3-modified nucleosome with histone H... -

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Entry
Database: PDB / ID: 8vnz
TitlePRC2_AJ1-450 bound to H3K36me3-modified nucleosome with histone H3 tail disengaged
Components
  • (Polycomb protein ...) x 2
  • Histone-binding protein RBBP4
  • Histone-lysine N-methyltransferase EZH2
  • Isoform 3 of Zinc finger protein AEBP2
  • Protein Jumonji
KeywordsGENE REGULATION / complex / methyltransferase / histone / epigenetics
Function / homology
Function and homology information


hepatocyte homeostasis / regulation of kidney development / cellular response to trichostatin A / negative regulation of striated muscle cell differentiation / regulation of gliogenesis / negative regulation of keratinocyte differentiation / random inactivation of X chromosome / [histone H3]-lysine27 N-trimethyltransferase / response to tetrachloromethane / CAF-1 complex ...hepatocyte homeostasis / regulation of kidney development / cellular response to trichostatin A / negative regulation of striated muscle cell differentiation / regulation of gliogenesis / negative regulation of keratinocyte differentiation / random inactivation of X chromosome / [histone H3]-lysine27 N-trimethyltransferase / response to tetrachloromethane / CAF-1 complex / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / negative regulation of retinoic acid receptor signaling pathway / histone H3K27 trimethyltransferase activity / cerebellar cortex development / primary miRNA binding / histone H3K27 methyltransferase activity / ubiquitin-modified histone reader activity / sex chromatin / positive regulation of cell cycle G1/S phase transition / NURF complex / regulatory ncRNA-mediated heterochromatin formation / cardiac muscle hypertrophy in response to stress / negative regulation of stem cell differentiation / facultative heterochromatin formation / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / regulation of stem cell differentiation / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / RSC-type complex / protein-lysine N-methyltransferase activity / oligodendrocyte differentiation / Polo-like kinase mediated events / chromatin silencing complex / Transcription of E2F targets under negative control by DREAM complex / pronucleus / positive regulation of dendrite development / histone H3K9me2/3 reader activity / DNA methylation-dependent constitutive heterochromatin formation / histone H3 methyltransferase activity / negative regulation of G1/S transition of mitotic cell cycle / G1 to G0 transition / synaptic transmission, GABAergic / histone methyltransferase activity / Sin3-type complex / negative regulation of gene expression, epigenetic / G1/S-Specific Transcription / spinal cord development / positive regulation of stem cell population maintenance / positive regulation of MAP kinase activity / lncRNA binding / histone deacetylase complex / negative regulation of transcription elongation by RNA polymerase II / positive regulation of protein serine/threonine kinase activity / histone methyltransferase complex / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / G0 and Early G1 / keratinocyte differentiation / subtelomeric heterochromatin formation / positive regulation of GTPase activity / negative regulation of cell differentiation / ribonucleoprotein complex binding / positive regulation of epithelial to mesenchymal transition / Cyclin E associated events during G1/S transition / RNA polymerase II core promoter sequence-specific DNA binding / pericentric heterochromatin / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Cyclin A:Cdk2-associated events at S phase entry / Regulation of TP53 Activity through Acetylation / nucleosome binding / heterochromatin / B cell differentiation / protein localization to chromatin / negative regulation of cytokine production involved in inflammatory response / liver regeneration / Deposition of new CENPA-containing nucleosomes at the centromere / negative regulation of cell migration / stem cell differentiation / hippocampus development / transcription corepressor binding / SUMOylation of chromatin organization proteins / Regulation of PTEN gene transcription / central nervous system development / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / brain development / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / ubiquitin binding / transcription coregulator activity / HDACs deacetylate histones / G1/S transition of mitotic cell cycle / negative regulation of transforming growth factor beta receptor signaling pathway / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / promoter-specific chromatin binding / cell population proliferation / chromatin DNA binding
Similarity search - Function
: / : / AEBP2-like, C-terminal SH3 domain / : / Polycomb protein SUZ12-like, Zn domain / EZH2, SET domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / Histone-lysine N-methyltransferase EZH1/EZH2 / Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domain ...: / : / AEBP2-like, C-terminal SH3 domain / : / Polycomb protein SUZ12-like, Zn domain / EZH2, SET domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / Histone-lysine N-methyltransferase EZH1/EZH2 / Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domain / Pre-SET CXC domain / : / WD repeat binding protein EZH2 / Polycomb repressive complex 2 tri-helical domain / CXC domain / Ezh2, MCSS domain / Tesmin/TSO1-like CXC domain / Tesmin/TSO1-like CXC domain / CXC domain / Histone-lysine N-methyltransferase EZH1/2-like / CXC domain profile. / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / : / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / ARID/BRIGHT DNA binding domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / JmjC domain, hydroxylase / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain superfamily / SET domain / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Polycomb protein EED / Histone-binding protein RBBP4 / Polycomb protein SUZ12 / Histone-lysine N-methyltransferase EZH2 / Zinc finger protein AEBP2 / Protein Jumonji
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCookis, T. / Nogales, E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM127018 United States
National Science Foundation (NSF, United States)GM-08295 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural basis for the inhibition of PRC2 by active transcription histone posttranslational modifications.
Authors: Trinity Cookis / Alexandria Lydecker / Paul Sauer / Vignesh Kasinath / Eva Nogales /
Abstract: Polycomb repressive complex 2 (PRC2) trimethylates histone H3 on K27 (H3K27me3) leading to gene silencing that is essential for embryonic development and maintenance of cell identity. PRC2 is ...Polycomb repressive complex 2 (PRC2) trimethylates histone H3 on K27 (H3K27me3) leading to gene silencing that is essential for embryonic development and maintenance of cell identity. PRC2 is regulated by protein cofactors and their crosstalk with histone modifications. Trimethylated histone H3 on K4 (H3K4me3) and K36 (H3K36me3) localize to sites of active transcription and inhibit PRC2 activity through unknown mechanisms. Using cryo-electron microscopy, we reveal that histone H3 tails containing H3K36me3 engage poorly with PRC2 and preclude its effective interaction with chromatin, while H3K4me3 binds to the allosteric site in the EED subunit, acting as an antagonist that competes with activators required for spreading of the H3K27me3 repressive mark. Thus, the location of the H3K4me3 and H3K36me3 modifications along the H3 tail allows them to target two requirements for efficient trimethylation of H3K27 by PRC2. We further show that the JARID2 cofactor modulates PRC2 activity in the presence of these histone modifications.
History
DepositionJan 14, 2024Deposition site: RCSB / Processing site: RCSB
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polycomb protein SUZ12
L: Polycomb protein EED
N: Histone-binding protein RBBP4
C: Histone-lysine N-methyltransferase EZH2
B: Protein Jumonji
P: Isoform 3 of Zinc finger protein AEBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)350,2537
Polymers349,8686
Non-polymers3841
Water00
1


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

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Components

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Polycomb protein ... , 2 types, 2 molecules AL

#1: Protein Polycomb protein SUZ12 / Chromatin precipitated E2F target 9 protein / ChET 9 protein / Joined to JAZF1 protein / Suppressor ...Chromatin precipitated E2F target 9 protein / ChET 9 protein / Joined to JAZF1 protein / Suppressor of zeste 12 protein homolog


Mass: 83181.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUZ12, CHET9, JJAZ1, KIAA0160 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15022
#2: Protein Polycomb protein EED / hEED / Embryonic ectoderm development protein / WD protein associating with integrin cytoplasmic ...hEED / Embryonic ectoderm development protein / WD protein associating with integrin cytoplasmic tails 1 / WAIT-1


Mass: 50267.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75530

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Protein , 4 types, 4 molecules NCBP

#3: Protein Histone-binding protein RBBP4 / Chromatin assembly factor 1 subunit C / CAF-1 subunit C / Chromatin assembly factor I p48 subunit / ...Chromatin assembly factor 1 subunit C / CAF-1 subunit C / Chromatin assembly factor I p48 subunit / CAF-I 48 kDa subunit / CAF-I p48 / Nucleosome-remodeling factor subunit RBAP48 / Retinoblastoma-binding protein 4 / RBBP-4 / Retinoblastoma-binding protein p48


Mass: 47709.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP4, RBAP48 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q09028
#4: Protein Histone-lysine N-methyltransferase EZH2 / ENX-1 / Enhancer of zeste homolog 2 / Lysine N-methyltransferase 6


Mass: 85492.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EZH2, KMT6 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q15910, [histone H3]-lysine27 N-trimethyltransferase
#5: Protein Protein Jumonji / Jumonji/ARID domain-containing protein 2


Mass: 49174.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JARID2, JMJ / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92833
#6: Protein Isoform 3 of Zinc finger protein AEBP2 / Adipocyte enhancer-binding protein 2 / AE-binding protein 2


Mass: 34042.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AEBP2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6ZN18

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Non-polymers , 1 types, 1 molecules

#7: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S

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Details

Has ligand of interestN
Has protein modificationY

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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: PRC2_AJ1-450 bound to H3K36me3-modified nucleosome / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Molecular weightValue: 0.35 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenConc.: 0.28 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 291 K

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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: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44519 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315134
ELECTRON MICROSCOPYf_angle_d0.58720595
ELECTRON MICROSCOPYf_dihedral_angle_d5.0642102
ELECTRON MICROSCOPYf_chiral_restr0.0432300
ELECTRON MICROSCOPYf_plane_restr0.0052668

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