5JVT: DNA binding domain of transcription factor FLI1

Crystal structure of the DNA binding domain of transcription factor FLI1 in complex with an 11-mer DNA GACCGGAAGTG. Determined by X-ray diffraction at 3.1 Å resolution. Released 14 Sept 2016.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Homo sapiens, Endothia gyrosa
Chains: 9
Atoms: 3,677
Mol. weight: 56.61 kDa
Ligands: PO4
Released: 14 Sept 2016

Explore 5JVT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5JVT contains 15 α-helices and 12 β-strands across 3 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	283-292	10
α-helix	294-296	3
β-strand	301-302	2	1
β-strand	308-310	3	1
α-helix	314-325	12
α-helix	332-341	10
β-strand	348-350	3	1
β-strand	357-360	4	1
α-helix	362-369	8

Chain D: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	283-292	10
α-helix	294-296	3
β-strand	301-302	2	2
β-strand	308-310	3	2
α-helix	314-324	11
α-helix	332-344	13
β-strand	348-350	3	2
β-strand	357-360	4	2
α-helix	362-368	7

Chain G: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	283-291	9
α-helix	294-298	5
β-strand	301-302	2	3
β-strand	308-310	3	3
α-helix	314-324	11
α-helix	332-341	10
β-strand	348-350	3	3
β-strand	357-360	4	3
α-helix	362-368	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Friend leukemia integration 1 transcription factor	A, D, G	protein	104	Homo sapiens	Q01543 (AlphaFold model)
DNA (5'-d(gpapcpcpgpgpapapgptp*g)-3')	B, E, H	DNA	11	Endothia gyrosa
DNA (5'-d(cpapcptptpcpcpgpgptp*c)-3')	C, F, I	DNA	11	Endothia gyrosa

Sequence of entity 1 (A, D, G), FASTA

>5JVT_1 Friend leukemia integration 1 transcription factor (chains A, D, G)
GPHMPGSGQIQLWQFLLELLSDSANASCITWEGTNGEFKMTDPDEVARRWGERKSKPNMN
YDKLSRALRYYYDKNIMTKVHGKRYAYKFDFHGIAQALQPHPTE

Sequence of entity 2 (B, E, H), FASTA

>5JVT_2 DNA (5'-D(*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*G)-3') (chains B, E, H)
GACCGGAAGTG

Sequence of entity 3 (C, F, I), FASTA

>5JVT_3 DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3') (chains C, F, I)
CACTTCCGGTC

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Structures of mithramycin analogues bound to DNA and implications for targeting transcription factor FLI1. Hou, C., Weidenbach, S., Cano, K.E. et al. Nucleic Acids Res (2016) 44:8990-9004. DOI 10.1093/nar/gkw761 · 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
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…
6VG2 3.9 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…

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