7JM5

Crystal structure of KDM4B in complex with QC6352


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Targeting KDM4 for treating PAX3-FOXO1-driven alveolar rhabdomyosarcoma.

Singh, S.Abu-Zaid, A.Jin, H.Fang, J.Wu, Q.Wang, T.Feng, H.Quarni, W.Shao, Y.Maxham, L.Abdolvahabi, A.Yun, M.K.Vaithiyalingam, S.Tan, H.Bowling, J.Honnell, V.Young, B.Guo, Y.Bajpai, R.Pruett-Miller, S.M.Grosveld, G.C.Hatley, M.Xu, B.Fan, Y.Wu, G.Chen, E.Y.Chen, T.Lewis, P.W.Rankovic, Z.Li, Y.Murphy, A.J.Easton, J.Peng, J.Chen, X.Wang, R.White, S.W.Davidoff, A.M.Yang, J.

(2022) Sci Transl Med 14: eabq2096-eabq2096

  • DOI: https://doi.org/10.1126/scitranslmed.abq2096
  • Primary Citation of Related Structures:  
    7JM5

  • PubMed Abstract: 

    Chimeric transcription factors drive lineage-specific oncogenesis but are notoriously difficult to target. Alveolar rhabdomyosarcoma (RMS) is an aggressive childhood soft tissue sarcoma transformed by the pathognomonic Paired Box 3-Forkhead Box O1 (PAX3-FOXO1) fusion protein, which governs a core regulatory circuitry transcription factor network. Here, we show that the histone lysine demethylase 4B (KDM4B) is a therapeutic vulnerability for PAX3-FOXO1 + RMS. Genetic and pharmacologic inhibition of KDM4B substantially delayed tumor growth. Suppression of KDM4 proteins inhibited the expression of core oncogenic transcription factors and caused epigenetic alterations of PAX3-FOXO1-governed superenhancers. Combining KDM4 inhibition with cytotoxic chemotherapy led to tumor regression in preclinical PAX3-FOXO1 + RMS subcutaneous xenograft models. In summary, we identified a targetable mechanism required for maintenance of the PAX3-FOXO1-related transcription factor network, which may translate to a therapeutic approach for fusion-positive RMS.


  • Organizational Affiliation

    Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine-specific demethylase 4B
A, B
367Homo sapiensMutation(s): 0 
Gene Names: KDM4BJHDM3BJMJD2BKIAA0876
EC: 1.14.11.66
UniProt & NIH Common Fund Data Resources
Find proteins for O94953 (Homo sapiens)
Explore O94953 
Go to UniProtKB:  O94953
PHAROS:  O94953
GTEx:  ENSG00000127663 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94953
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.825α = 90
b = 97.107β = 106.516
c = 80.068γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA229739

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-08-17
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description