8GDX

Crystal structure of JADE1 PZP domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Guiding the HBO1 complex function through the JADE subunit.

Gaurav, N.Kanai, A.Lachance, C.Cox, K.L.Liu, J.Grzybowski, A.T.Saksouk, N.Klein, B.J.Komata, Y.Asada, S.Ruthenburg, A.J.Poirier, M.G.Cote, J.Yokoyama, A.Kutateladze, T.G.

(2024) Nat Struct Mol Biol 31: 1039-1049

  • DOI: https://doi.org/10.1038/s41594-024-01245-2
  • Primary Citation of Related Structures:  
    8GDX, 8GE0

  • PubMed Abstract: 

    JADE is a core subunit of the HBO1 acetyltransferase complex that regulates developmental and epigenetic programs and promotes gene transcription. Here we describe the mechanism by which JADE facilitates recruitment of the HBO1 complex to chromatin and mediates its enzymatic activity. Structural, genomic and complex assembly in vivo studies show that the PZP (PHD1-zinc-knuckle-PHD2) domain of JADE engages the nucleosome through binding to histone H3 and DNA and is necessary for the association with chromatin targets. Recognition of unmethylated H3K4 by PZP directs enzymatic activity of the complex toward histone H4 acetylation, whereas H3K4 hypermethylation alters histone substrate selectivity. We demonstrate that PZP contributes to leukemogenesis, augmenting transforming activity of the NUP98-JADE2 fusion. Our findings highlight biological consequences and the impact of the intact JADE subunit on genomic recruitment, enzymatic function and pathological activity of the HBO1 complex.


  • Organizational Affiliation

    Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein Jade-1174Homo sapiensMutation(s): 0 
Gene Names: JADE1KIAA1807PHF17
UniProt & NIH Common Fund Data Resources
Find proteins for Q6IE81 (Homo sapiens)
Explore Q6IE81 
Go to UniProtKB:  Q6IE81
PHAROS:  Q6IE81
GTEx:  ENSG00000077684 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IE81
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.439α = 90
b = 81.439β = 90
c = 81.439γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Database references
  • Version 1.2: 2024-07-31
    Changes: Database references