7AT8

Histone H3 recognition by nucleosome-bound PRC2 subunit EZH2.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 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

Structural basis for PRC2 decoding of active histone methylation marks H3K36me2/3.

Finogenova, K.Bonnet, J.Poepsel, S.Schafer, I.B.Finkl, K.Schmid, K.Litz, C.Strauss, M.Benda, C.Muller, J.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.61964
  • Primary Citation of Related Structures:  
    7AT8

  • PubMed Abstract: 

    Repression of genes by Polycomb requires that PRC2 modifies their chromatin by trimethylating lysine 27 on histone H3 (H3K27me3). At transcriptionally active genes, di- and tri-methylated H3K36 inhibit PRC2. Here, the cryo-EM structure of PRC2 on dinucleosomes reveals how binding of its catalytic subunit EZH2 to nucleosomal DNA orients the H3 N-terminus via an extended network of interactions to place H3K27 into the active site. Unmodified H3K36 occupies a critical position in the EZH2-DNA interface. Mutation of H3K36 to arginine or alanine inhibits H3K27 methylation by PRC2 on nucleosomes in vitro . Accordingly, Drosophila H3K36A and H3K36R mutants show reduced levels of H3K27me3 and defective Polycomb repression of HOX genes. The relay of interactions between EZH2, the nucleosomal DNA and the H3 N-terminus therefore creates the geometry that permits allosteric inhibition of PRC2 by methylated H3K36 in transcriptionally active chromatin.


  • Organizational Affiliation

    Max Planck Institute of Biochemistry, Laboratory of Chromatin Biology, Martinsried, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2764Homo sapiensMutation(s): 0 
Gene Names: EZH2KMT6
EC: 2.1.1.356
UniProt & NIH Common Fund Data Resources
Find proteins for Q15910 (Homo sapiens)
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PHAROS:  Q15910
GTEx:  ENSG00000106462 
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UniProt GroupQ15910
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb protein SUZ12B [auth C]739Homo 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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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2C [auth D],
G [auth H]
135Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4D [auth E],
H [auth I]
102Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2AE [auth F],
I [auth J]
129Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591
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UniProt GroupP06897
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1F [auth G],
J [auth K]
122Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
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Entity ID: 7
MoleculeChains LengthOrganismImage
Widom601 DNA plus linkerK [auth T]156synthetic construct
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Entity ID: 8
MoleculeChains LengthOrganismImage
Widom601 DNA plus linkerL [auth U]156synthetic construct
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
T [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
M [auth A]
N [auth A]
O [auth A]
P [auth A]
Q [auth A]
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
SAH BindingDB:  7AT8 IC50: min: 263, max: 6.50e+4 (nM) from 17 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB1064
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Database references