7KSR

PRC2:EZH1_A from a dimeric PRC2 bound to a 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 1.2 of the entry. See complete history


Literature

Structures of monomeric and dimeric PRC2:EZH1 reveal flexible modules involved in chromatin compaction.

Grau, D.Zhang, Y.Lee, C.H.Valencia-Sanchez, M.Zhang, J.Wang, M.Holder, M.Svetlov, V.Tan, D.Nudler, E.Reinberg, D.Walz, T.Armache, K.J.

(2021) Nat Commun 12: 714-714

  • DOI: https://doi.org/10.1038/s41467-020-20775-z
  • Primary Citation of Related Structures:  
    7KSO, 7KSR, 7KTP, 7KTQ

  • PubMed Abstract: 

    Polycomb repressive complex 2 (PRC2) is a histone methyltransferase critical for maintaining gene silencing during eukaryotic development. In mammals, PRC2 activity is regulated in part by the selective incorporation of one of two paralogs of the catalytic subunit, EZH1 or EZH2. Each of these enzymes has specialized biological functions that may be partially explained by differences in the multivalent interactions they mediate with chromatin. Here, we present two cryo-EM structures of PRC2:EZH1, one as a monomer and a second one as a dimer bound to a nucleosome. When bound to nucleosome substrate, the PRC2:EZH1 dimer undergoes a dramatic conformational change. We demonstrate that mutation of a divergent EZH1/2 loop abrogates the nucleosome-binding and methyltransferase activities of PRC2:EZH1. Finally, we show that PRC2:EZH1 dimers are more effective than monomers at promoting chromatin compaction, and the divergent EZH1/2 loop is essential for this function, thereby tying together the methyltransferase, nucleosome-binding, and chromatin-compaction activities of PRC2:EZH1. We speculate that the conformational flexibility and the ability to dimerize enable PRC2 to act on the varied chromatin substrates it encounters in the cell.


  • Organizational Affiliation

    Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase EZH1747Homo sapiensMutation(s): 0 
Gene Names: EZH1KIAA0388
EC: 2.1.1.356
UniProt & NIH Common Fund Data Resources
Find proteins for Q92800 (Homo sapiens)
Explore Q92800 
Go to UniProtKB:  Q92800
PHAROS:  Q92800
GTEx:  ENSG00000108799 
Entity Groups  
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UniProt GroupQ92800
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-binding protein RBBP4B [auth D]425Homo sapiensMutation(s): 0 
Gene Names: RBBP4RBAP48
UniProt & NIH Common Fund Data Resources
Find proteins for Q09028 (Homo sapiens)
Explore Q09028 
Go to UniProtKB:  Q09028
PHAROS:  Q09028
GTEx:  ENSG00000162521 
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UniProt GroupQ09028
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb protein SUZ12739Homo sapiensMutation(s): 0 
Gene Names: SUZ12CHET9JJAZ1KIAA0160
UniProt & NIH Common Fund Data Resources
Find proteins for Q15022 (Homo sapiens)
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PHAROS:  Q15022
GTEx:  ENSG00000178691 
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UniProt GroupQ15022
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb protein EEDD [auth B]441Homo sapiensMutation(s): 0 
Gene Names: EED
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Find proteins for O75530 (Homo sapiens)
Explore O75530 
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PHAROS:  O75530
GTEx:  ENSG00000074266 
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UniProt GroupO75530
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 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 StatesR01 GM115882

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-03
    Type: Initial release
  • Version 1.1: 2021-02-24
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references