Crystal structure of JARID1A-PHD3 complexed with H3(1-9)K4me3 peptide

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report

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Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger.

Wang, G.G.Song, J.Wang, Z.Dormann, H.L.Casadio, F.Li, H.Luo, J.L.Patel, D.J.Allis, C.D.

(2009) Nature 459: 847-851

  • DOI: https://doi.org/10.1038/nature08036
  • Primary Citation of Related Structures:  
    2KGG, 2KGI, 3GL6

  • PubMed Abstract: 

    Histone H3 lysine 4 methylation (H3K4me) has been proposed as a critical component in regulating gene expression, epigenetic states, and cellular identities1. The biological meaning of H3K4me is interpreted by conserved modules including plant homeodomain (PHD) fingers that recognize varied H3K4me states. The dysregulation of PHD fingers has been implicated in several human diseases, including cancers and immune or neurological disorders. Here we report that fusing an H3K4-trimethylation (H3K4me3)-binding PHD finger, such as the carboxy-terminal PHD finger of PHF23 or JARID1A (also known as KDM5A or RBBP2), to a common fusion partner nucleoporin-98 (NUP98) as identified in human leukaemias, generated potent oncoproteins that arrested haematopoietic differentiation and induced acute myeloid leukaemia in murine models. In these processes, a PHD finger that specifically recognizes H3K4me3/2 marks was essential for leukaemogenesis. Mutations in PHD fingers that abrogated H3K4me3 binding also abolished leukaemic transformation. NUP98-PHD fusion prevented the differentiation-associated removal of H3K4me3 at many loci encoding lineage-specific transcription factors (Hox(s), Gata3, Meis1, Eya1 and Pbx1), and enforced their active gene transcription in murine haematopoietic stem/progenitor cells. Mechanistically, NUP98-PHD fusions act as 'chromatin boundary factors', dominating over polycomb-mediated gene silencing to 'lock' developmentally critical loci into an active chromatin state (H3K4me3 with induced histone acetylation), a state that defined leukaemia stem cells. Collectively, our studies represent, to our knowledge, the first report that deregulation of the PHD finger, an 'effector' of specific histone modification, perturbs the epigenetic dynamics on developmentally critical loci, catastrophizes cellular fate decision-making, and even causes oncogenesis during mammalian development.

  • Organizational Affiliation

    Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, New York 10065, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone demethylase JARID1A52Homo sapiensMutation(s): 0 
EC: 1.14.11
UniProt & NIH Common Fund Data Resources
Find proteins for P29375 (Homo sapiens)
Explore P29375 
Go to UniProtKB:  P29375
GTEx:  ENSG00000073614 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29375
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H39Homo sapiensMutation(s): 0 
Find proteins for Q92133 (Xenopus laevis)
Explore Q92133 
Go to UniProtKB:  Q92133
Entity Groups  
UniProt GroupQ92133
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.222 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.95α = 90
b = 49.95β = 90
c = 86.45γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance