6VG8

Crystal structure of the DNA binding domains of human FLI1 and Runx2 in complex with 16-mer DNA CAGAGGATGTGGCTTC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.31 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.274 

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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:  
    6VG2, 6VG8, 6VGD, 6VGE, 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)  |  3D 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01543
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Runt-related transcription factor 2D123Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13950
Protein Feature View
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  • Reference Sequence

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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
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  • Reference Sequence

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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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.31 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.274 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.427α = 90
b = 104.427β = 90
c = 326.382γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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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