6C23

Cryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in the Compact Active State


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Structures of human PRC2 with its cofactors AEBP2 and JARID2.

Kasinath, V.Faini, M.Poepsel, S.Reif, D.Feng, X.A.Stjepanovic, G.Aebersold, R.Nogales, E.

(2018) Science 359: 940-944

  • DOI: https://doi.org/10.1126/science.aar5700
  • Primary Citation of Related Structures:  
    6C23, 6C24

  • PubMed Abstract: 

    Transcriptionally repressive histone H3 lysine 27 methylation by Polycomb repressive complex 2 (PRC2) is essential for cellular differentiation and development. Here we report cryo-electron microscopy structures of human PRC2 in a basal state and two distinct active states while in complex with its cofactors JARID2 and AEBP2. Both cofactors mimic the binding of histone H3 tails. JARID2, methylated by PRC2, mimics a methylated H3 tail to stimulate PRC2 activity, whereas AEBP2 interacts with the RBAP48 subunit, mimicking an unmodified H3 tail. SUZ12 interacts with all other subunits within the assembly and thus contributes to the stability of the complex. Our analysis defines the complete architecture of a functionally relevant PRC2 and provides a structural framework to understand its regulation by cofactors, histone tails, and RNA.


  • Organizational Affiliation

    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb protein SUZ12A,
E [auth M],
I [auth Q]
739Homo sapiensMutation(s): 0 
Gene Names: SUZ12CHET9JJAZ1KIAA0160
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Find proteins for Q15022 (Homo sapiens)
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GTEx:  ENSG00000178691 
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UniProt GroupQ15022
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein JumonjiB [auth E]348Homo sapiensMutation(s): 0 
Gene Names: JARID2JMJ
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Find proteins for Q92833 (Homo sapiens)
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Go to UniProtKB:  Q92833
GTEx:  ENSG00000008083 
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UniProt GroupQ92833
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase EZH2C [auth K],
K [auth C]
746Homo sapiensMutation(s): 0 
Gene Names: EZH2KMT6
EC: 2.1.1.43
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Find proteins for Q15910 (Homo sapiens)
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GTEx:  ENSG00000106462 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb protein EEDD [auth L]441Homo sapiensMutation(s): 0 
Gene Names: EED
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GTEx:  ENSG00000074266 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-binding protein RBBP4F [auth N]425Homo sapiensMutation(s): 0 
Gene Names: RBBP4RBAP48
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Find proteins for Q09028 (Homo sapiens)
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GTEx:  ENSG00000162521 
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UniProt GroupQ09028
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
JARID2-substrateG [auth O]7Homo sapiensMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger protein AEBP2H [auth P]295Homo sapiensMutation(s): 0 
Gene Names: AEBP2
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GTEx:  ENSG00000139154 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
SUZ12J [auth Z]135Homo sapiensMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Protein JumonjiL [auth B]345Homo sapiensMutation(s): 0 
Gene Names: JARID2JMJ
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Find proteins for Q92833 (Homo sapiens)
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GTEx:  ENSG00000008083 
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Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M3L
Query on M3L
L [auth B]L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
European Research Council (ERC)European Union233226
European Research Council (ERC)European Union670821

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-24
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Database references
  • Version 1.2: 2018-02-14
    Changes: Author supporting evidence
  • Version 1.3: 2018-03-07
    Changes: Database references
  • Version 1.4: 2018-10-03
    Changes: Data collection, Refinement description
  • Version 1.5: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.6: 2019-12-18
    Changes: Other