7DW5

Crystal structure of DUX4 HD1-HD2 domain complexed with ERG sites

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

DNA crosslinking and recombination-activating genes 1/2 (RAG1/2) are required for oncogenic splicing in acute lymphoblastic leukemia.

Zhang, H., Cheng, N., Li, Z., Bai, L., Fang, C., Li, Y., Zhang, W., Dong, X., Jiang, M., Liang, Y., Zhang, S., Mi, J., Zhu, J., Zhang, Y., Chen, S.J., Zhao, Y., Weng, X.Q., Hu, W., Chen, Z., Huang, J., Meng, G.

(2021) Cancer Commun (Lond) 41: 1116-1136

  • DOI: https://doi.org/10.1002/cac2.12234
  • Primary Citation of Related Structures:  
    7DW5

  • PubMed Abstract: 

    Abnormal alternative splicing is frequently associated with carcinogenesis. In B-cell acute lymphoblastic leukemia (B-ALL), double homeobox 4 fused with immunoglobulin heavy chain (DUX4/IGH) can lead to the aberrant production of E-26 transformation-specific family related gene abnormal transcript (ERG alt ) and other splicing variants. However, the molecular mechanism underpinning this process remains elusive. Here, we aimed to know how DUX4/IGH triggers abnormal splicing in leukemia.

    • Organizational Affiliation: 

    Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, Shanghai, 200025, P. R. China.


Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Double homeobox protein 4-like protein 2
A, B
150Homo sapiensMutation(s): 0 
Gene Names: DUX4L2
UniProt
Find proteins for P0CJ85 (Homo sapiens)
Explore P0CJ85 
Go to UniProtKB:  P0CJ85
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CJ85
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*GP*AP*CP*TP*TP*GP*AP*TP*GP*AP*GP*AP*TP*TP*AP*GP*AP*CP*TP*G)-3')C [auth E],
E [auth C]		21Homo sapiens
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*GP*AP*CP*TP*TP*GP*AP*TP*GP*AP*GP*AP*TP*TP*AP*GP*AP*CP*TP*G)-3')D [auth F],
F [auth D]		21Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR
Download Ideal Coordinates CCD File 
G [auth E]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.974α = 95.82
b = 64.451β = 92.55
c = 69.432γ = 103.31
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81770142
National Natural Science Foundation of China (NSFC)China81970132

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description