9MX8: DNA binding domain of FLI1

Crystal structure of the DNA binding domain of FLI1 in complex with a DNA containing three contiguous GGAA sites. Determined by X-ray diffraction at 3.15 Å resolution. Released 12 Mar 2025.

Method: X-ray diffraction
Resolution: 3.15 Å
Organisms: Homo sapiens, synthetic construct
Chains: 5
Atoms: 3,190
Mol. weight: 53.24 kDa
Released: 12 Mar 2025

Explore 9MX8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MX8 contains 18 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: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	266-272	7
α-helix	283-291	9
β-strand	300-302	3	1
β-strand	308-311	4	1
α-helix	314-324	11
α-helix	332-340	9
α-helix	342-345	4
β-strand	348-350	3	1
β-strand	357-360	4	1
α-helix	362-369	8

Chain C: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	283-291	9
α-helix	294-296	3
β-strand	300-302	3	2
β-strand	308-311	4	2
α-helix	314-324	11
α-helix	332-345	14
β-strand	348-350	3	2
β-strand	357-360	4	2
α-helix	362-366	5

Chain D: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	280-282	3
α-helix	283-292	10
α-helix	294-296	3
β-strand	300-302	3	3
β-strand	308-311	4	3
α-helix	314-325	12
α-helix	332-340	9
α-helix	342-345	4
β-strand	348-350	3	3
β-strand	357-360	4	3
α-helix	362-369	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Friend leukemia integration 1 transcription factor	A, C, D	protein	121	Homo sapiens	Q01543 (AlphaFold model)
DNA (5'-d(pgpapcpcpgpgpapapgpgpapapgpgpapapgptp*g)-3')	E	DNA	19	synthetic construct
DNA (5'-d(cpapcptptpcpcptptpcpcptptpcpcpgpgptp*c)-3')	F	DNA	19	synthetic construct

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

>9MX8_1 Friend leukemia integration 1 transcription factor (chains A, C, D)
GPHMQPDPYQILGPTSSRLANPGSGQIQLWQFLLELLSDSANASCITWEGTNGEFKMTDP
DEVARRWGERKSKPNMNYDKLSRALRYYYDKNIMTKVHGKRYAYKFDAHGIAQALQPHPT
E

Sequence of entity 2 (E), FASTA

>9MX8_2 DNA (5'-D(P*GP*AP*CP*CP*GP*GP*AP*AP*GP*GP*AP*AP*GP*GP*AP*AP*GP*TP*G)-3') (chains E)
GACCGGAAGGAAGGAAGTG

Sequence of entity 3 (F), FASTA

>9MX8_3 DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*TP*TP*CP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3') (chains F)
CACTTCCTTCCTTCCGGTC

Primary citation

Structure and cooperative formation of a FLI1 filament on contiguous GGAA DNA sites. Hou, C., Tsodikov, O.V. Nucleic Acids Res (2025) 53. DOI 10.1093/nar/gkaf205 · 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…
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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