8TAS

PRC2 monomer bound to nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Activation of automethylated PRC2 by dimerization on chromatin.

Sauer, P.V.Pavlenko, E.Cookis, T.Zirden, L.C.Renn, J.Singhal, A.Hunold, P.Hoehne-Wiechmann, M.N.van Ray, O.Kaschani, F.Kaiser, M.Hansel-Hertsch, R.Sanbonmatsu, K.Y.Nogales, E.Poepsel, S.

(2024) Mol Cell 

  • DOI: https://doi.org/10.1016/j.molcel.2024.08.025
  • Primary Citation of Related Structures:  
    8T9G, 8TAS, 8TB9

  • PubMed Abstract: 

    Polycomb repressive complex 2 (PRC2) is an epigenetic regulator that trimethylates lysine 27 of histone 3 (H3K27me3) and is essential for embryonic development and cellular differentiation. H3K27me3 is associated with transcriptionally repressed chromatin and is established when PRC2 is allosterically activated upon methyl-lysine binding by the regulatory subunit EED. Automethylation of the catalytic subunit enhancer of zeste homolog 2 (EZH2) stimulates its activity by an unknown mechanism. Here, we show that human PRC2 forms a dimer on chromatin in which an inactive, automethylated PRC2 protomer is the allosteric activator of a second PRC2 that is poised to methylate H3 of a substrate nucleosome. Functional assays support our model of allosteric trans-autoactivation via EED, suggesting a previously unknown mechanism mediating context-dependent activation of PRC2. Our work showcases the molecular mechanism of auto-modification-coupled dimerization in the regulation of chromatin-modifying complexes.


  • Organizational Affiliation

    California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb protein SUZ12A [auth D]619Homo sapiensMutation(s): 0 
Gene Names: SUZ12CHET9JJAZ1KIAA0160
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PHAROS:  Q15022
GTEx:  ENSG00000178691 
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UniProt GroupQ15022
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase EZH2B [auth E]753Homo sapiensMutation(s): 0 
Gene Names: EZH2KMT6
EC: 2.1.1.356
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Find proteins for Q15910 (Homo sapiens)
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PHAROS:  Q15910
GTEx:  ENSG00000106462 
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UniProt GroupQ15910-2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb protein EEDC [auth G]441Homo sapiensMutation(s): 0 
Gene Names: EED
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Find proteins for O75530 (Homo sapiens)
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PHAROS:  O75530
GTEx:  ENSG00000074266 
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UniProt GroupO75530
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2D [auth I],
L [auth W]
136Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P84233 (Xenopus laevis)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4F [auth J],
M [auth X]
106Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2AG [auth R],
J [auth U]
133Xenopus laevisMutation(s): 0 
Gene Names: h2ac14.L
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1H [auth S],
K [auth V]
123Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-binding protein RBBP4N [auth O]425Homo sapiensMutation(s): 0 
Gene Names: RBBP4RBAP48
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GTEx:  ENSG00000162521 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger protein AEBP2O [auth Y]303Homo sapiensMutation(s): 0 
Gene Names: AEBP2
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PHAROS:  Q6ZN18
GTEx:  ENSG00000139154 
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UniProt GroupQ6ZN18
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (226-MER)E [auth H]215synthetic construct
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Entity ID: 9
MoleculeChains LengthOrganismImage
DNA (226-MER)I [auth T]215synthetic construct
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
P [auth E]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-25
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Database references, Structure summary