6VGG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.31 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 

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Ligand Structure Quality Assessment 


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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional regulator ERGA128Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11308
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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
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UniProt GroupQ13950
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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
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UniProt GroupQ13951
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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
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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
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QWP (Subject of Investigation/LOI)
Query on QWP

Download Ideal Coordinates CCD File 
F [auth B],
H [auth C]
mithramycin
C52 H76 O24
CFCUWKMKBJTWLW-BKHRDMLASA-N
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
G [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.31 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.678α = 90
b = 104.678β = 90
c = 322.836γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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