8VML | pdb_00008vml

PRC2_AJ1-450 bound to H3K4me3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for the inhibition of PRC2 by active transcription histone posttranslational modifications.

Cookis, T.Lydecker, A.Sauer, P.Kasinath, V.Nogales, E.

(2025) Nat Struct Mol Biol 32: 393-404

  • DOI: https://doi.org/10.1038/s41594-024-01452-x
  • Primary Citation of Related Structures:  
    8VMI, 8VMJ, 8VML, 8VMN, 8VNV, 8VNZ, 8VO0, 8VOB

  • PubMed 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 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.


  • Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SUZ12739Homo 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
JARID21,246Homo sapiensMutation(s): 0 
Gene Names: JARID2JMJ
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PHAROS:  Q92833
GTEx:  ENSG00000008083 
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UniProt GroupQ92833
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
EZH2746Homo sapiensMutation(s): 0 
Gene Names: EZH2KMT6
EC: 2.1.1.356
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GTEx:  ENSG00000106462 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3D [auth I]22Homo sapiensMutation(s): 0 
Gene Names: 
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UniProt GroupP68431
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
EEDE [auth L]441Homo sapiensMutation(s): 0 
Gene Names: EED
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GTEx:  ENSG00000074266 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RBAP48F [auth N]425Homo sapiensMutation(s): 0 
Gene Names: RBBP4RBAP48
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GTEx:  ENSG00000162521 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
AEPB2G [auth P]301Homo sapiensMutation(s): 0 
Gene Names: AEBP2
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PHAROS:  Q6ZN18
GTEx:  ENSG00000139154 
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Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M3L
Query on M3L
B
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35-GM127018
National Science Foundation (NSF, United States)United StatesGM-08295

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release
  • Version 1.1: 2025-01-22
    Changes: Data collection, Database references
  • Version 1.2: 2025-03-05
    Changes: Data collection, Database references