6WKR

PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

JARID2 and AEBP2 regulate PRC2 in the presence of H2AK119ub1 and other histone modifications.

Kasinath, V., Beck, C., Sauer, P., Poepsel, S., Kosmatka, J., Faini, M., Toso, D., Aebersold, R., Nogales, E.

(2021) Science 371

  • DOI: https://doi.org/10.1126/science.abc3393
  • Primary Citation of Related Structures:  
    6WKR

  • PubMed Abstract: 

    • 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 ...

    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.

    Organizational Affiliation: 

    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinA [auth T],
Q [auth F]		76Homo sapiensMutation(s): 1 
Gene Names: UBC
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UniProt GroupP0CG48
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Polycomb protein SUZ12B [auth A]739Homo sapiensMutation(s): 0 
Gene Names: SUZ12, CHET9, JJAZ1, KIAA0160
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Polycomb protein EEDC [auth L]441Homo sapiensMutation(s): 0 
Gene Names: EED
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-binding protein RBBP4D [auth N]425Homo sapiensMutation(s): 0 
Gene Names: RBBP4, RBAP48
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase EZH2E [auth C]746Homo sapiensMutation(s): 0 
Gene Names: EZH2, KMT6
EC: 2.1.1.356
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Protein JumonjiF [auth B],
R [auth E]		450Homo sapiensMutation(s): 0 
Gene Names: JARID2, JMJ
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc finger protein AEBP2G [auth P]295Homo sapiensMutation(s): 0 
Gene Names: AEBP2
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2I,
M [auth O]		136Xenopus laevisMutation(s): 0 
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Entity ID: 10
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Histone H4J,
N [auth Q]		103Xenopus laevisMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1K,
O [auth R]		130Xenopus laevisMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1L [auth M],
P [auth S]		126Xenopus laevisMutation(s): 1 
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (314-MER)320Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH
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T [auth C]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N		 Ligand Interaction
ZN (Subject of Investigation/LOI)
Query on ZN
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U [auth P]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG
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S [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L		F [auth B],
R [auth E]		L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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 StatesGM127018

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-03
    Type: Initial release