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- EMDB-76903: PRC2(EZH2 WT) AJ106-350 in the extended active state -

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Basic information

Entry
Database: EMDB / ID: EMD-76903
TitlePRC2(EZH2 WT) AJ106-350 in the extended active state
Map data
Sample
  • Complex: Polycomb Repressive Complex 2
KeywordsPRC2 / Polycomb / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsMatyas MN / Kasinath V / Lewis PW
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM155426 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00GM132544 United States
National Science Foundation (NSF, United States)2446197 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R24OD033699 United States
CitationJournal: bioRxiv / Year: 2026
Title: EZH2 Serine 21 Phosphorylation Restrains Compact-State PRC2 Activation and H3K27me3 Propagation.
Authors: Andrew Q Rashoff / Mark Matyas / Elizabeth G Porter / Ryen Hazzard / Benjamin A Garcia / Vignesh Kasinath / Peter W Lewis
Abstract: Polycomb Repressive Complex 2 (PRC2) propagates H3K27me3 through EED-dependent allosteric activation, yet how cells modulate the magnitude of this positive-feedback response remains poorly understood. ...Polycomb Repressive Complex 2 (PRC2) propagates H3K27me3 through EED-dependent allosteric activation, yet how cells modulate the magnitude of this positive-feedback response remains poorly understood. Here, we identify phosphorylation of EZH2 serine 21 as a post-translational mechanism that attenuates PRC2 allosteric responsiveness. Prior structural studies have established that activator-bound PRC2 adopts both compact and extended active conformations. Using cryo-EM classification of wild-type and phospho-null EZH2 S21A PRC2 complexes, we find that the phospho-null EZH2 S21A substitution changes the distribution of particles across these pre-existing states, shifting PRC2 from a predominantly extended conformation to one enriched for the compact, allosterically activated conformation. Consistent with this structural transition, EZH2 S21A increases basal PRC2 activity, lowers the EC for H3K27me3-dependent stimulation, and accelerates H3K27me3 accumulation on peptide and nucleosome substrates. Disruption of the EED-EZH2 interface suppresses the S21A gain-of-activity phenotype, indicating that S21 phosphorylation constrains PRC2 by limiting productive EED-EZH2 allosteric coupling. In mesenchymal stem cells, loss of this phosphorylation-dependent restraint broadens H3K27me3 domains, reduces canonical PRC1 enrichment at high-occupancy Polycomb target loci, misregulates lineage-associated transcriptional programs, and impairs differentiation. These findings identify EZH2 S21 phosphorylation as a molecular rheostat that limits compact-state PRC2 activation, constrains H3K27me3 spreading, and preserves Polycomb-dependent developmental competence.
History
DepositionApr 24, 2026-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76903.png

Downloads & links

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Map

FileDownload / File: emd_76903.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 384 pix.
= 289.958 Å		0.76 Å/pix.
x 384 pix.
= 289.958 Å		0.76 Å/pix.
x 384 pix.
= 289.958 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7551 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0265
Minimum - Maximum-0.15239352 - 0.33739015
Average (Standard dev.)0.0006834198 (±0.00751474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 289.9584 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_76903_additional_1.map
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Half map: #1

Fileemd_76903_half_map_1.map
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Half map: #2

Fileemd_76903_half_map_2.map
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Sample components

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Entire : Polycomb Repressive Complex 2

EntireName: Polycomb Repressive Complex 2
Components
  • Complex: Polycomb Repressive Complex 2

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Supramolecule #1: Polycomb Repressive Complex 2

SupramoleculeName: Polycomb Repressive Complex 2 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 308 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

Concentration1 mg/mL
BufferpH: 7.9 / Component - Concentration: 150.0 mM / Component - Formula: NaCl / Component - Name: sodium chloride / Details: 150mM Nacl, 25mM HEPES, 1mM TCEP, 10% glycerol
GridModel: Quantifoil R2/1 / Material: GOLD / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 1.5 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (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: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

7335

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 119130
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.7.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.7.1)
Final 3D classificationNumber classes: 6 / Avg.num./class: 70000 / Software - Name: cryoSPARC (ver. 4.7.1)
FSC plot (resolution estimation)

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