PHF23 PHD Domain Apo

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.241 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Mechanistic insights into chromatin targeting by leukemic NUP98-PHF23 fusion.

Zhang, Y.Guo, Y.Gough, S.M.Zhang, J.Vann, K.R.Li, K.Cai, L.Shi, X.Aplan, P.D.Wang, G.G.Kutateladze, T.G.

(2020) Nat Commun 11: 3339-3339

  • DOI: https://doi.org/10.1038/s41467-020-17098-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Chromosomal NUP98-PHF23 translocation is associated with an aggressive form of acute myeloid leukemia (AML) and poor survival rate. Here, we report the molecular mechanisms by which NUP98-PHF23 recognizes the histone mark H3K4me3 and is inhibited by small molecule compounds, including disulfiram that directly targets the PHD finger of PHF23 (PHF23PHD). Our data support a critical role for the PHD fingers of NUP98-PHF23, and related NUP98-KDM5A and NUP98-BPTF fusions in driving leukemogenesis, and demonstrate that blocking this interaction in NUP98-PHF23 expressing AML cells leads to cell death through necrotic and late apoptosis pathways. An overlap of NUP98-KDM5A oncoprotein binding sites and H3K4me3-positive loci at the Hoxa/b gene clusters and Meis1 in ChIP-seq, together with NMR analysis of the H3K4me3-binding sites of the PHD fingers from PHF23, KDM5A and BPTF, suggests a common PHD finger-dependent mechanism that promotes leukemogenesis by this type of NUP98 fusions. Our findings highlight the direct correlation between the abilities of NUP98-PHD finger fusion chimeras to associate with H3K4me3-enriched chromatin and leukemic transformation.

  • Organizational Affiliation

    Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHD finger protein 23
A, B, C, D, E
61Homo sapiensMutation(s): 0 
Gene Names: PHF23
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BUL5 (Homo sapiens)
Explore Q9BUL5 
Go to UniProtKB:  Q9BUL5
GTEx:  ENSG00000040633 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BUL5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.241 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.916α = 90
b = 66.916β = 90
c = 151.048γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-15
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Advisory, Data collection, Database references, Refinement description