5Z6Z

Crystal structure of human DUX4 homeodomains bound to DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural basis for multiple gene regulation by human DUX4.

Li, Y., Wu, B., Liu, H., Gao, Y., Yang, C., Chen, X., Zhang, J., Chen, Y., Gu, Y., Li, J., Ma, J., Gan, J.

(2018) Biochem Biophys Res Commun 505: 1161-1167

  • DOI: 10.1016/j.bbrc.2018.10.056
  • Primary Citation of Related Structures:  
    5Z6Z, 5ZFZ, 5ZFY, 5ZFW

  • PubMed Abstract: 

    • DUX4 plays critical role in the molecular pathogenesis of the neuromuscular disorder facioscapulohumeral muscular dystrophy and acute lymphoblastic leukemia in humans. As a master transcription regulator, DUX4 can also bind the promoters and activate the transcription of hundreds ZGA-associated genes ...

    DUX4 plays critical role in the molecular pathogenesis of the neuromuscular disorder facioscapulohumeral muscular dystrophy and acute lymphoblastic leukemia in humans. As a master transcription regulator, DUX4 can also bind the promoters and activate the transcription of hundreds ZGA-associated genes. Here we report on the structural and biochemical studies of DUX4 double homeodomains (DUX4-DH), representing the only structures contain both homeodomain 1 (HD1) and homeodomain 2 (HD2). HD1 and HD2 adopt classical homeobox fold; via the helix inserted into the major groove and the N-terminal extended loop inserted into the minor groove, HD1 and HD2 recognize the box1 (5'-TAA-3') and box2 (5'-TGA-3') nucleotides of the consensus sequence, respectively. Among the box1 and box2 linking nucleotides (CCTAA), the two adenine residues are reported to be highly conserved; however, they are not directly recognized by DUX4-DH in the structures. Besides different nucleotides, our ITC analysis indicated that DUX4-DH can also tolerate various changes in the linker length. Our studies not only revealed the basis for target DNA recognition by DUX4, but also advanced our understanding on multiple gene activation by DUX4.

    Organizational Affiliation: 

    State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China. Electronic address: ganjhh@fudan.edu.cn.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Double homeobox protein 4A153Homo sapiensMutation(s): 0 
Gene Names: DUX4, DUX10
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBX2 (Homo sapiens)
Explore Q9UBX2 
Go to UniProtKB:  Q9UBX2
PHAROS:  Q9UBX2
GTEx:  ENSG00000260596
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*CP*AP*CP*TP*AP*AP*CP*CP*TP*AP*AP*TP*CP*AP*CP*AP*CP*C)-3')B [auth D]19synthetic construct
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*GP*TP*GP*TP*GP*AP*TP*TP*AP*GP*GP*TP*TP*AP*GP*TP*GP*G)-3')C [auth E]19synthetic construct
      Protein Feature View
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      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.30 Å
      • R-Value Free: 0.251 
      • R-Value Work: 0.211 
      • R-Value Observed: 0.213 
      • Space Group: P 32 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 64.879α = 90
      b = 64.879β = 90
      c = 152.075γ = 120
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling
      PHASERphasing

      Structure Validation

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      View more in-depth experimental data

      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2018-10-31
        Type: Initial release
      • Version 1.1: 2018-11-14
        Changes: Data collection, Database references