5JVT

Crystal structure of the DNA binding domain of transcription factor FLI1 in complex with an 11-mer DNA GACCGGAAGTG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of mithramycin analogues bound to DNA and implications for targeting transcription factor FLI1.

Hou, C.Weidenbach, S.Cano, K.E.Wang, Z.Mitra, P.Ivanov, D.N.Rohr, J.Tsodikov, O.V.

(2016) Nucleic Acids Res 44: 8990-9004

  • DOI: 10.1093/nar/gkw761
  • Primary Citation of Related Structures:  
    5JW2, 5JVT, 5JVW, 5JW0

  • PubMed Abstract: 
  • Transcription factors have been considered undruggable, but this paradigm has been recently challenged. DNA binding natural product mithramycin (MTM) is a potent antagonist of oncogenic transcription factor EWS-FLI1. Structural details of MTM recognition of DNA, including the FLI1 binding sequence GGA(A/T), are needed to understand how MTM interferes with EWS-FLI1 ...

    Transcription factors have been considered undruggable, but this paradigm has been recently challenged. DNA binding natural product mithramycin (MTM) is a potent antagonist of oncogenic transcription factor EWS-FLI1. Structural details of MTM recognition of DNA, including the FLI1 binding sequence GGA(A/T), are needed to understand how MTM interferes with EWS-FLI1. We report a crystal structure of an MTM analogue MTM SA-Trp bound to a DNA oligomer containing a site GGCC, and two structures of a novel analogue MTM SA-Phe in complex with DNA. MTM SA-Phe is bound to sites AGGG and GGGT on one DNA, and to AGGG and GGGA(T) (a FLI1 binding site) on the other, revealing how MTM recognizes different DNA sequences. Unexpectedly, at sub-micromolar concentrations MTMs stabilize FLI1-DNA complex on GGAA repeats, which are critical for the oncogenic function of EWS-FLI1. We also directly demonstrate by nuclear magnetic resonance formation of a ternary FLI1-DNA-MTM complex on a single GGAA FLI1/MTM binding site. These biochemical and structural data and a new FLI1-DNA structure suggest that MTM binds the minor groove and perturbs FLI1 bound nearby in the major groove. This ternary complex model may lead to development of novel MTM analogues that selectively target EWS-FLI1 or other oncogenic transcription factors, as anti-cancer therapeutics.


    Organizational Affiliation

    Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA oleg.tsodikov@uky.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Friend leukemia integration 1 transcription factorA, D, G104Homo sapiensMutation(s): 0 
Gene Names: FLI1
UniProt & NIH Common Fund Data Resources
Find proteins for Q01543 (Homo sapiens)
Explore Q01543 
Go to UniProtKB:  Q01543
PHAROS:  Q01543
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*G)-3')B, E, H11Endothia gyrosa
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3')C, F, I11Endothia gyrosa
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      PO4
      Query on PO4

      Download Ideal Coordinates CCD File 
      J [auth D]PHOSPHATE ION
      O4 P
      NBIIXXVUZAFLBC-UHFFFAOYSA-K
       Ligand Interaction
      GOL
      Query on GOL

      Download Ideal Coordinates CCD File 
      K [auth G]GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.10 Å
      • R-Value Free: 0.237 
      • R-Value Work: 0.194 
      • R-Value Observed: 0.196 
      • Space Group: P 61 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 191.845α = 90
      b = 191.845β = 90
      c = 87.556γ = 120
      Software Package:
      Software NamePurpose
      REFMACrefinement
      HKL-2000data reduction
      HKL-2000data scaling
      MOLREPphasing

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2016-09-14
        Type: Initial release
      • Version 1.1: 2016-10-26
        Changes: Database references