6VGE

Crystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), in complex with 16mer DNA CAGAGGATGTGGCTTC

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.25 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.313 
  • R-Value Observed: 0.313 

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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: https://doi.org/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. 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator ERG128Homo sapiensMutation(s): 0 
Gene Names: ERG
UniProt & NIH Common Fund Data Resources
Find proteins for P11308 (Homo sapiens)
Explore P11308 
Go to UniProtKB:  P11308
PHAROS:  P11308
GTEx:  ENSG00000157554 
Entity Groups  
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UniProt GroupP11308
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Runt-related transcription factor 2177Homo sapiensMutation(s): 0 
Gene Names: RUNX2, AML3, CBFA1, OSF2, PEBP2A
UniProt & NIH Common Fund Data Resources
Find proteins for Q13950 (Homo sapiens)
Explore Q13950 
Go to UniProtKB:  Q13950
PHAROS:  Q13950
GTEx:  ENSG00000124813 
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UniProt GroupQ13950
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Entity ID: 5
MoleculeChains Sequence 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
GTEx:  ENSG00000067955 
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UniProt GroupQ13951
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3')16Homo sapiens
Sequence Annotations
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*TP*G)-3')16Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.25 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.313 
  • R-Value Observed: 0.313 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.917α = 90
b = 103.917β = 90
c = 322.912γ = 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
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description