6VGD

Crystal structure of the DNA binding domain (DBD) of human FLI1 and the complex of the DBD of human Runx2 with core binding factor beta (Cbfb), in complex with 16mer DNA CAGAGGATGTGGCTTC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.295 
  • R-Value Observed: 0.295 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Allosteric interference in oncogenic FLI1 and ERG transactions by mithramycins.

Hou, C.Mandal, A.Rohr, J.Tsodikov, O.V.

(2021) Structure 29: 404-412.e4

  • DOI: 10.1016/j.str.2020.11.012
  • Primary Citation of Related Structures:  
    6VGD, 6VGE, 6VG8, 6VG2, 6VGG

  • PubMed Abstract: 
  • ETS family transcription factors of ERG and FLI1 play a key role in oncogenesis of prostate cancer and Ewing sarcoma by binding regulatory DNA sites and interfering with function of other factors. Mithramycin (MTM) is an anti-cancer, DNA binding natural product that functions as a potent antagonist of ERG and FLI1 by an unknown mechanism ...

    ETS family transcription factors of ERG and FLI1 play a key role in oncogenesis of prostate cancer and Ewing sarcoma by binding regulatory DNA sites and interfering with function of other factors. Mithramycin (MTM) is an anti-cancer, DNA binding natural product that functions as a potent antagonist of ERG and FLI1 by an unknown mechanism. We present a series of crystal structures of the DNA binding domain (DBD) of ERG/FLI1 culminating in a structure of a high-order complex of the ERG/FLI1 DBD, transcription factor Runx2, core-binding factor beta (Cbfβ), and MTM on a DNA enhancer site, along with supporting DNA binding studies using MTM and its analogues. Taken together, these data provide insight into allosteric mechanisms underlying ERG and FLI1 transactions and their disruption by MTM analogues.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Friend leukemia integration 1 transcription factorA104Homo 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Runt-related transcription factor 2D177Homo sapiensMutation(s): 0 
Gene Names: RUNX2AML3CBFA1OSF2PEBP2A
UniProt & NIH Common Fund Data Resources
Find proteins for Q13950 (Homo sapiens)
Explore Q13950 
Go to UniProtKB:  Q13950
PHAROS:  Q13950
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Core-binding factor subunit betaE [auth G]156Homo sapiensMutation(s): 0 
Gene Names: CBFB
UniProt & NIH Common Fund Data Resources
Find proteins for Q13951 (Homo sapiens)
Explore Q13951 
Go to UniProtKB:  Q13951
PHAROS:  Q13951
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3')B16Homo sapiens
    Protein Feature View
    Expand
    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*TP*G)-3')C16Homo sapiens
      Protein Feature View
      Expand
      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 4.20 Å
      • R-Value Free: 0.293 
      • R-Value Work: 0.295 
      • R-Value Observed: 0.295 
      • Space Group: P 62 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 104.513α = 90
      b = 104.513β = 90
      c = 322.04γ = 120
      Software Package:
      Software NamePurpose
      REFMACrefinement
      PDB_EXTRACTdata extraction
      HKL-2000data reduction
      HKL-2000data scaling
      PHASERphasing

      Structure Validation

      View Full Validation Report




      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      Department of Defense (DOD, United States)United StatesPC150300P1
      Department of Defense (DOD, United States)United StatesPC150300P2

      Revision History  (Full details and data files)

      • Version 1.0: 2020-11-25
        Type: Initial release
      • Version 1.1: 2020-12-16
        Changes: Database references
      • Version 1.2: 2021-05-19
        Changes: Database references