6VGD image
Deposition Date 2020-01-07
Release Date 2020-11-25
Last Version Date 2023-10-11
Entry Detail
PDB ID:
6VGD
Keywords:
TRANSCRIPTION
Title:
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
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Escherichia coli BL21(DE3)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
4.20 Å
R-Value Free:
0.29
R-Value Work:
0.29
R-Value Observed:
0.29
Space Group:
P 62 2 2
6VGD validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Friend leukemia integration 1 transcription factor
Gene (Uniprot):FLI1
Chain IDs:A
Chain Length:104
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q01543 Pfam ID:PF00178
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3')
Chain IDs:B
Chain Length:16
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*TP*G)-3')
Chain IDs:C
Chain Length:16
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Runt-related transcription factor 2
Gene (Uniprot):RUNX2
Chain IDs:D
Chain Length:177
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13950 Pfam ID:PF00853
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Core-binding factor subunit beta
Gene (Uniprot):CBFB
Chain IDs:E (auth: G)
Chain Length:156
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13951 Pfam ID:PF02312
Ligand Molecules
NA
Primary Citation
Allosteric interference in oncogenic FLI1 and ERG transactions by mithramycins.
Structure 29 404 412.e4 (2021)
PMID: 33275876 DOI: 10.1016/j.str.2020.11.012

Abstact

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.

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Primary Citation of related structures
6VGD