6WKR image
Deposition Date 2020-04-16
Release Date 2021-02-03
Last Version Date 2025-06-04
Entry Detail
PDB ID:
6WKR
Keywords:
GENE REGULATION/DNA
Title:
PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Xenopus laevis (Taxon ID: 8355)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6WKR validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Polycomb protein SUZ12
Gene (Uniprot):SUZ12
Chain IDs:B (auth: A)
Chain Length:739
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q15022 Pfam ID:PF09733
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein Jumonji
Gene (Uniprot):JARID2
Chain IDs:F (auth: B), R (auth: E)
Chain Length:450
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:Q92833
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone-lysine N-methyltransferase EZH2
Gene (Uniprot):EZH2
Chain IDs:E (auth: C)
Chain Length:746
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q15910 Pfam ID:PF11616, PF18118, PF21358, PF18264, PF00856 EC:2.1.1.356
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (314-MER)
Chain IDs:H
Chain Length:320
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H3.2
Chain IDs:I, M (auth: O)
Chain Length:136
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P84233 Pfam ID:PF00125
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H4
Chain IDs:J, N (auth: Q)
Chain Length:103
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P62799 Pfam ID:PF15511
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1
Chain IDs:K, O (auth: R)
Chain Length:130
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P06897 Pfam ID:PF00125, PF16211
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Polycomb protein EED
Gene (Uniprot):EED
Chain IDs:C (auth: L)
Chain Length:441
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O75530 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2B 1.1
Chain IDs:L (auth: M), P (auth: S)
Chain Length:126
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P02281 Pfam ID:PF00125
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone-binding protein RBBP4
Gene (Uniprot):RBBP4
Chain IDs:D (auth: N)
Chain Length:425
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q09028 Pfam ID:PF12265, PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Zinc finger protein AEBP2
Gene (Uniprot):AEBP2
Chain IDs:G (auth: P)
Chain Length:295
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q6ZN18
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin
Gene (Uniprot):UBC
Chain IDs:A (auth: T), Q (auth: F)
Chain Length:76
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P0CG48 Pfam ID:PF00240
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
M3L F LYS modified residue
Ligand Molecules
MG
SAH
ZN
Primary Citation
JARID2 and AEBP2 regulate PRC2 in the presence of H2AK119ub1 and other histone modifications.
Science 371 ? ? (2021)
PMID: 33479123 DOI: 10.1126/science.abc3393

Abstact

Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) cooperate to determine cell identity by epigenetic gene expression regulation. However, the mechanism of PRC2 recruitment by means of recognition of PRC1-mediated H2AK119ub1 remains poorly understood. Our PRC2 cryo-electron microscopy structure with cofactors JARID2 and AEBP2 bound to a H2AK119ub1-containing nucleosome reveals a bridge helix in EZH2 that connects the SET domain, H3 tail, and nucleosomal DNA. JARID2 and AEBP2 each interact with one ubiquitin and the H2A-H2B surface. JARID2 stimulates PRC2 through interactions with both the polycomb protein EED and the H2AK119-ubiquitin, whereas AEBP2 has an additional scaffolding role. The presence of these cofactors partially overcomes the inhibitory effect that H3K4me3 and H3K36me3 exert on core PRC2 (in the absence of cofactors). Our results support a key role for JARID2 and AEBP2 in the cross-talk between histone modifications and PRC2 activity.

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Primary Citation of related structures
6WKR