6V3Y

Crystal structure of EED in complex with PALI1-K1219me3 peptide

  • Classification: GENE REGULATION
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-11-26 Released: 2021-05-26 
  • Deposition Author(s): Zhang, Q., Davidovich, C.
  • Funding Organization(s): Australian Research Council (ARC), National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

PALI1 facilitates DNA and nucleosome binding by PRC2 and triggers an allosteric activation of catalysis.

Zhang, Q.Agius, S.C.Flanigan, S.F.Uckelmann, M.Levina, V.Owen, B.M.Davidovich, C.

(2021) Nat Commun 12: 4592-4592

  • DOI: https://doi.org/10.1038/s41467-021-24866-3
  • Primary Citation of Related Structures:  
    6V3X, 6V3Y

  • PubMed Abstract: 

    The polycomb repressive complex 2 (PRC2) is a histone methyltransferase that maintains cell identities. JARID2 is the only accessory subunit of PRC2 that known to trigger an allosteric activation of methyltransferase. Yet, this mechanism cannot be generalised to all PRC2 variants as, in vertebrates, JARID2 is mutually exclusive with most of the accessory subunits of PRC2. Here we provide functional and structural evidence that the vertebrate-specific PRC2 accessory subunit PALI1 emerged through a convergent evolution to mimic JARID2 at the molecular level. Mechanistically, PRC2 methylates PALI1 K1241, which then binds to the PRC2-regulatory subunit EED to allosterically activate PRC2. PALI1 K1241 is methylated in mouse and human cell lines and is essential for PALI1-induced allosteric activation of PRC2. High-resolution crystal structures revealed that PALI1 mimics the regulatory interactions formed between JARID2 and EED. Independently, PALI1 also facilitates DNA and nucleosome binding by PRC2. In acute myelogenous leukemia cells, overexpression of PALI1 leads to cell differentiation, with the phenotype altered by a separation-of-function PALI1 mutation, defective in allosteric activation and active in DNA binding. Collectively, we show that PALI1 facilitates catalysis and substrate binding by PRC2 and provide evidence that subunit-induced allosteric activation is a general property of holo-PRC2 complexes.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb protein EED359Homo sapiensMutation(s): 0 
Gene Names: EED
UniProt & NIH Common Fund Data Resources
Find proteins for O75530 (Homo sapiens)
Explore O75530 
Go to UniProtKB:  O75530
PHAROS:  O75530
GTEx:  ENSG00000074266 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75530
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PALI1 peptide5Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96JN0 (Homo sapiens)
Explore Q96JN0 
Go to UniProtKB:  Q96JN0
PHAROS:  Q96JN0
GTEx:  ENSG00000196233 
Entity Groups  
UniProt GroupQ96JN0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M3L
Query on M3L
B
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.775α = 90
b = 85.296β = 90
c = 91.106γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata processing
SCALAdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDE180100219
Australian Research Council (ARC)AustraliaDP190103407
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1162921

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2021-08-04
    Changes: Database references
  • Version 1.2: 2021-08-25
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Refinement description