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- EMDB-43360: H3K4me3 nucleosome bound to PRC2_AJ1-450 -

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Basic information

Entry
Database: EMDB / ID: EMD-43360
TitleH3K4me3 nucleosome bound to PRC2_AJ1-450
Map data
Sample
  • Complex: H3K4me3 nucleosome core particle bound to PRC2_AJ1-450
    • DNA: DNA (157-MER)
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • Protein or peptide: Histone H3.2
    • DNA: DNA (157-MER)
Keywordsnucleosome / histone / chromatin / epigenetics / GENE REGULATION / GENE REGULATION-DNA complex
Function / homology
Function and homology information


negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine ...negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / chromosome, telomeric region / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane
Similarity search - Function
: / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A ...: / Histone H2B signature. / Histone H2A conserved site / Histone H2A 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 / 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
Similarity search - Domain/homology
Histone H2B / Histone H4 / Histone H2A / Histone H3.2
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCookis T / Nogales E
Funding support United States, 2 items
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 13, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43360.png

Downloads & links

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Map

FileDownload / File: emd_43360.map.gz / Format: CCP4 / Size: 411.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 476 pix.
= 409.36 Å		0.86 Å/pix.
x 476 pix.
= 409.36 Å		0.86 Å/pix.
x 476 pix.
= 409.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.283
Minimum - Maximum-0.87928194 - 1.5718197
Average (Standard dev.)0.0004261234 (±0.03433216)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions476476476
Spacing476476476
CellA=B=C: 409.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43360_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43360_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : H3K4me3 nucleosome core particle bound to PRC2_AJ1-450

EntireName: H3K4me3 nucleosome core particle bound to PRC2_AJ1-450
Components
  • Complex: H3K4me3 nucleosome core particle bound to PRC2_AJ1-450
    • DNA: DNA (157-MER)
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • Protein or peptide: Histone H3.2
    • DNA: DNA (157-MER)

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Supramolecule #1: H3K4me3 nucleosome core particle bound to PRC2_AJ1-450

SupramoleculeName: H3K4me3 nucleosome core particle bound to PRC2_AJ1-450
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA (157-MER)

MacromoleculeName: DNA (157-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.71798 KDa
SequenceString: (DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DG)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC) ...String:
(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DG)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC) (DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DT) (DA)(DA) (DA)(DC)(DG)(DC)(DG)(DG)(DG) (DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG) (DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DG)(DC)(DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG) (DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA) (DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG) (DC)(DC)(DT)(DG)(DG)(DG)(DC)(DA)(DC)(DC) (DG)(DG)(DG)(DA)(DT)(DT) (DC)(DT)(DC) (DC)(DA)(DG)(DC)(DC)(DG)(DC)(DC)(DG)(DG) (DC)(DA)(DG)(DC)

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Macromolecule #7: DNA (157-MER)

MacromoleculeName: DNA (157-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.246703 KDa
SequenceString: (DG)(DC)(DT)(DG)(DC)(DC)(DG)(DG)(DC)(DG) (DG)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT) (DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC) (DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC) (DA) (DA)(DT)(DT)(DG)(DG)(DT) ...String:
(DG)(DC)(DT)(DG)(DC)(DC)(DG)(DG)(DC)(DG) (DG)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT) (DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC) (DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC) (DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG) (DT)(DA)(DG)(DA)(DC)(DA)(DG)(DC)(DT)(DC) (DT)(DA) (DG)(DC)(DA)(DC)(DC)(DG)(DC) (DT)(DT)(DA)(DA)(DA)(DC)(DG)(DC)(DA)(DC) (DG)(DT)(DA) (DC)(DG)(DC)(DG)(DC)(DT) (DG)(DT)(DC)(DC)(DC)(DC)(DC)(DG)(DC)(DG) (DT)(DT)(DT)(DA) (DA)(DA)(DC)(DC)(DG) (DC)(DC)(DA)(DA)(DG)(DG)(DG)(DG)(DA)(DT) (DT)(DA)(DC)(DT)(DC) (DC)(DC)(DT)(DA) (DG)(DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DC) (DA)(DC)(DG)(DT)(DC)(DT) (DC)(DA)(DG) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA)(DT) (DC)(DC)(DT)(DG)

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Macromolecule #2: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.463183 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MART(M3L)QTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIA QDF KTDLRFQSSA VMALQEASEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.2

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Macromolecule #3: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #4: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.797794 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKAKTRSSRA GLQFPVGRVH RLLRKGNYAE RVGAGAPVYL AAVLEYLTAE ILELAGNAAR DNKKTRIIPR HLQLAVRNDE ELNKLLGRV TIAQGGVLPN IQSVLLPKC

UniProtKB: Histone H2A

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Macromolecule #5: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 10.764405 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RKTRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAV TKYTSAK

UniProtKB: Histone H2B

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Macromolecule #6: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.421101 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

21707

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102257
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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