6U81

Crystal Structure of the Double Homeodomain of DUX4 in Complex with a DNA aptamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD.

Klingler, C.Ashley, J.Shi, K.Stiefvater, A.Kyba, M.Sinnreich, M.Aihara, H.Kinter, J.

(2020) FASEB J 34: 4573-4590

  • DOI: 10.1096/fj.201902696
  • Primary Citation of Related Structures:  
    6U81, 6U82

  • PubMed Abstract: 
  • Aberrant expression of the transcription factor double homeobox protein 4 (DUX4) can lead to a number of diseases including facio-scapulo-humeral muscular dystrophy (FSHD), acute lymphoblastic leukemia, and sarcomas. Inhibition of DUX4 may represent a therapeutic strategy for these diseases ...

    Aberrant expression of the transcription factor double homeobox protein 4 (DUX4) can lead to a number of diseases including facio-scapulo-humeral muscular dystrophy (FSHD), acute lymphoblastic leukemia, and sarcomas. Inhibition of DUX4 may represent a therapeutic strategy for these diseases. By applying Systematic Evolution of Ligands by EXponential Enrichment (SELEX), we identified aptamers against DUX4 with specific secondary structural elements conveying high affinity to DUX4 as assessed by fluorescence resonance energy transfer and fluorescence polarization techniques. Sequences analysis of these aptamers revealed the presence of two consensus DUX4 motifs in a reverse complementary fashion forming hairpins interspersed with bulge loops at distinct positions that enlarged the binding surface with the DUX4 protein, as determined by crystal structure analysis. We demonstrate that insertion of specific structural elements into transcription factor binding oligonucleotides can enhance specificity and affinity.


    Organizational Affiliation

    Neuromuscular Research Group, Department of Biomedicine, University Hospital Basel, Basel, Switzerland.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Double homeobox protein 4A132Homo sapiensMutation(s): 0 
Gene Names: DUX4DUX10
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBX2 (Homo sapiens)
Explore Q9UBX2 
Go to UniProtKB:  Q9UBX2
PHAROS:  Q9UBX2
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*CP*GP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*AP*AP*CP*A)-3')B17Homo sapiens
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*GP*TP*TP*GP*AP*TP*TP*AP*GP*CP*CP*CP*AP*TP*TP*AP*CP*GP*C)-3')C20Homo sapiens
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      EDO (Subject of Investigation/LOI)
      Query on EDO

      Download Ideal Coordinates CCD File 
      D [auth A], E [auth A]1,2-ETHANEDIOL
      C2 H6 O2
      LYCAIKOWRPUZTN-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.34 Å
      • R-Value Free: 0.247 
      • R-Value Work: 0.216 
      • R-Value Observed: 0.218 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 71.64α = 90
      b = 73.19β = 90
      c = 108.07γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      XDSdata reduction
      XDSdata scaling
      PHENIXphasing

      Structure Validation

      View Full Validation Report



      Ligand Structure Quality Assessment  



      Entry History & Funding Information

      Deposition Data

      • Deposited Date: 2019-09-04 
      • Released Date: 2020-02-19 
      • Deposition Author(s): Shi, K., Aihara, H.

      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118047

      Revision History  (Full details and data files)

      • Version 1.0: 2020-02-19
        Type: Initial release
      • Version 1.1: 2020-02-26
        Changes: Derived calculations
      • Version 1.2: 2020-03-18
        Changes: Database references