7AT8 | pdb_00007at8

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

Validation slider image for 7AT8

This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 375.67 kDa 
  • Atom Count: 15,951 
  • Modeled Residue Count: 1,510 
  • Deposited Residue Count: 2,791 
  • Unique protein chains: 6
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
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)
Explore Q15910 
Go to UniProtKB:  Q15910
PHAROS:  Q15910
GTEx:  ENSG00000106462 
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UniProt GroupQ15910
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Reference Sequence
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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)
Explore Q15022 
Go to UniProtKB:  Q15022
PHAROS:  Q15022
GTEx:  ENSG00000178691 
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UniProt GroupQ15022
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Reference Sequence
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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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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H4D [auth E],
H [auth I]
102Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
Explore P62799 
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UniProt GroupP62799
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2AE [auth F],
I [auth J]
129Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591
UniProt
Find proteins for P06897 (Xenopus laevis)
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UniProt GroupP06897
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Reference Sequence
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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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UniProt GroupP02281
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 7
MoleculeChains LengthOrganismImage
Widom601 DNA plus linkerK [auth T]156synthetic construct
Sequence Annotations
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Reference Sequence
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Entity ID: 8
MoleculeChains LengthOrganismImage
Widom601 DNA plus linkerL [auth U]156synthetic construct
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Reference Sequence

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

Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



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
  • Version 1.2: 2025-12-10
    Changes: Data collection, Structure summary