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- EMDB-47133: PRC2_AJ119-450, JARID2_107-121 / Nuc_unmodified -

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Basic information

Entry
Database: EMDB / ID: EMD-47133
TitlePRC2_AJ119-450, JARID2_107-121 / Nuc_unmodified
Map data
Sample
  • Complex: PRC2_AJ119-450 bound to JARID2_107-121 peptide and unmodified nucleosome substrate
Keywordscomplex / methyltransferase / histone / epigenetics / GENE REGULATION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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
DepositionSep 26, 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_47133.png

Downloads & links

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Map

FileDownload / File: emd_47133.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 384 pix.
= 437.76 Å		1.14 Å/pix.
x 384 pix.
= 437.76 Å		1.14 Å/pix.
x 384 pix.
= 437.76 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.074
Minimum - Maximum-0.11947608 - 0.4955746
Average (Standard dev.)0.00040466167 (±0.014734574)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 437.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: locally filtered map of local refinement PRC2

Fileemd_47133_additional_1.map
Annotationlocally filtered map of local refinement PRC2
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Additional map: local refinement of PRC2

Fileemd_47133_additional_2.map
Annotationlocal refinement of PRC2
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Additional map: #1

Fileemd_47133_additional_3.map
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Additional map: #2

Fileemd_47133_additional_4.map
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Half map: #1

Fileemd_47133_half_map_1.map
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Half map: #2

Fileemd_47133_half_map_2.map
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Sample components

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Entire : PRC2_AJ119-450 bound to JARID2_107-121 peptide and unmodified nuc...

EntireName: PRC2_AJ119-450 bound to JARID2_107-121 peptide and unmodified nucleosome substrate
Components
  • Complex: PRC2_AJ119-450 bound to JARID2_107-121 peptide and unmodified nucleosome substrate

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Supramolecule #1: PRC2_AJ119-450 bound to JARID2_107-121 peptide and unmodified nuc...

SupramoleculeName: PRC2_AJ119-450 bound to JARID2_107-121 peptide and unmodified nucleosome substrate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 350 KDa

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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

Concentration0.28 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 291 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 4720 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

21707

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 73778
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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