6VG2: PDB entry 6VG2

Name: PDB 6VG2: Crystal structure of the DNA binding domain of human transcription factor FLI1 in complex with 16-mer DNA CAGAGGATGTGGCTTC
Published: 2020-11-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Crystal structure of the DNA binding domain of human transcription factor FLI1 in complex with 16-mer DNA CAGAGGATGTGGCTTC. Determined by X-ray diffraction at 3.9 Å resolution. Released 25 Nov 2020.

Method: X-ray diffraction
Resolution: 3.9 Å
Organism: Homo sapiens
Chains: 6
Atoms: 2,824
Mol. weight: 43.79 kDa
Released: 25 Nov 2020

Explore 6VG2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VG2 contains 10 α-helices and 8 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	283-291	9
α-helix	294-298	5
β-strand	301-302	2	1
β-strand	308-310	3	1
α-helix	316-324	9
α-helix	332-340	9
β-strand	348-350	3	1
β-strand	357-360	4	1
α-helix	362-368	7

Chain D: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	283-291	9
β-strand	301-302	2	2
β-strand	308-310	3	2
α-helix	314-322	9
α-helix	332-339	8
β-strand	348-350	3	2
α-helix	351	1
β-strand	357-360	4	2
α-helix	362-367	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Friend leukemia integration 1 transcription factor	A, D	protein	104	Homo sapiens	Q01543 (AlphaFold model)
DNA (5'-d(gpapcpcpgpgpapapgptpgpgpcptptpc)-3')	B, E	DNA	16	Homo sapiens
DNA (5'-d(gpapapgpcpcpapcptptpcpcpgpgptpc)-3')	C, F	DNA	16	Homo sapiens

Sequence of entity 1 (A, D), FASTA

>6VG2_1 Friend leukemia integration 1 transcription factor (chains A, D)
GPHMPGSGQIQLWQFLLELLSDSANASCITWEGTNGEFKMTDPDEVARRWGERKSKPNMN
YDKLSRALRYYYDKNIMTKVHGKRYAYKFDFHGIAQALQPHPTE

Sequence of entity 2 (B, E), FASTA

>6VG2_2 DNA (5'-D(*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP*GP*CP*TP*TP*C)-3') (chains B, E)
CAGAGGATGTGGCTTC

Sequence of entity 3 (C, F), FASTA

>6VG2_3 DNA (5'-D(*GP*AP*AP*GP*CP*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3') (chains C, F)
GAAGCCACATCCTCTG

Primary citation

Allosteric interference in oncogenic FLI1 and ERG transactions by mithramycins. Hou, C., Mandal, A., Rohr, J. et al. Structure (2021) 29:404-412.e4. DOI 10.1016/j.str.2020.11.012 · PubMed

Other PDB entries of the same protein (UniProt Q01543 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9CP6 1.66 Å, Crystal structure of the DNA binding domain of FLI1 (residues 259-371)
9MX9 2.55 Å, Crystal structure of the DNA binding domain of FLI1 (F362A) in complex with a DNA…
9MXA 2.59 Å, Crystal structure of the DNA binding domain of FLI1 (wild-type) in complex with a DNA…
5E8G 2.7 Å, Crystal structure of the DNA binding domain of human transcription factor FLI1
5JVT 3.1 Å, Crystal structure of the DNA binding domain of transcription factor FLI1 in complex with…
9MX8 3.15 Å, Crystal structure of the DNA binding domain of FLI1 in complex with a DNA containing…
9MWY 3.28 Å, Crystal structure of the DNA binding domain of FLI1 in complex with a DNA containing…
5E8I 3.45 Å, Crystal structure of the DNA binding domain of human transcription factor FLI1 in…
6VGD 4.2 Å, Crystal structure of the DNA binding domain (DBD) of human FLI1 and the complex of the…
6VG8 4.31 Å, Crystal structure of the DNA binding domains of human FLI1 and Runx2 in complex with…
1FLI DNA-binding domain of fli-1
1X66 Solution structure of the SAM_PNT-domain of the human friend LEUKEMIAINTEGRATION 1…

Browse structure collections

About this viewer

MolViewer shows 6VG2 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.