7KTQ

Nucleosome from a dimeric PRC2 bound to a nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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 H3
A, E
99Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18002543mg
UniProt
Find proteins for P84233 (Xenopus laevis)
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Go to UniProtKB:  P84233
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UniProt GroupP84233
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
79Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A
C, G
105Xenopus laevisMutation(s): 0 
Gene Names: h2ac14.Lh2ac14hist1h2ajLOC494591XELAEV_18003602mg
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis)
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UniProt GroupQ6AZJ8
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B
D, H
95Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18032685mg
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 5
MoleculeChains LengthOrganismImage
601 DNA (167-MER)167Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
601 DNA (167-MER)167Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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