› 6vgd

X-ray diffraction
4.2Å resolution

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

Released:
DOI: 10.2210/pdb6vgd/pdb
PDB entry 6vgd coloured by chain, front view.
PDB entry 6vgd coloured by chain, side view.
PDB entry 6vgd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Allosteric interference in oncogenic FLI1 and ERG transactions by mithramycins.
Hou C, Mandal A, Rohr J, Tsodikov OV
Structure 29 404-412.e4 (2021)
PMID: 33275876

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-120773 (preferred)
Entry contents:
3 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (5 distinct):
Friend leukemia integration 1 transcription factor Chain: A
Molecule details ›
Chain: A
Length: 104 amino acids
Theoretical weight: 12.1 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q01543 (Residues: 276-375; Coverage: 22%)
Gene name: FLI1
Sequence domains: Ets-domain
Runt-related transcription factor 2 Chain: D
Molecule details ›
Chain: D
Length: 177 amino acids
Theoretical weight: 19.54 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q13950 (Residues: 111-287; Coverage: 34%)
Gene names: AML3, CBFA1, OSF2, PEBP2A, RUNX2
Sequence domains: Runt domain
Core-binding factor subunit beta Chain: G
Molecule details ›
Chain: G
Length: 156 amino acids
Theoretical weight: 18.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q13951 (Residues: 1-142; Coverage: 78%)
Gene name: CBFB
Sequence domains: Core binding factor beta subunit
DNA (5'-D(P*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 16 nucleotides
Theoretical weight: 4.95 KDa
DNA (5'-D(P*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*TP*G)-3') Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.84 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P6222
Unit cell:
a: 104.513Å b: 104.513Å c: 322.04Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.295 0.295 0.293
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Current insights into the role of Fli-1 in hematopoiesis and malignant transformation.
Ben-David et al. (2022)
1 more

1 mention without citation

Allosteric interference in oncogenic FLI1 and ERG transactions by mithramycins.
Hou et al. (2021)