6VG8: DNA binding domains of human FLI1 and Runx2

Crystal structure of the DNA binding domains of human FLI1 and Runx2 in complex with 16-mer DNA CAGAGGATGTGGCTTC. Determined by X-ray diffraction at 4.31 Å resolution. Released 25 Nov 2020.

Method: X-ray diffraction
Resolution: 4.31 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,376
Mol. weight: 35.6 kDa
Released: 25 Nov 2020

Explore 6VG8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VG8 contains 5 α-helices and 16 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	284-287	4
α-helix	294-296	3
β-strand	300-302	3	1
β-strand	309-311	3	1
α-helix	314-325	12
α-helix	332-345	14
β-strand	348-350	3	1
β-strand	358-360	3	1
α-helix	362-365	4

Chain D: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	113-114	2	2
β-strand	121-124	4	2
β-strand	129-131	3	3
β-strand	140-144	5	2
β-strand	153-157	5	4
β-strand	168-169	2	5
β-strand	172-174	3	4
β-strand	179-182	4	2
β-strand	186-187	2	5
β-strand	200-204	5	4
β-strand	209-210	2	4
β-strand	218-220	3	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Friend leukemia integration 1 transcription factor	A	protein	104	Homo sapiens	Q01543 (AlphaFold model)
DNA (5'-d(pcpapgpapgpgpaptpgptpgpgpcptptpc)-3')	B	DNA	16	Homo sapiens
DNA (5'-d(pgpapapgpcpcpapcpaptpcpcptpcptpg)-3')	C	DNA	16	Homo sapiens
Runt-related transcription factor 2	D	protein	123	Homo sapiens	Q13950 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6VG8_1 Friend leukemia integration 1 transcription factor (chains A)
GPHMPGSGQIQLWQFLLELLSDSANASCITWEGTNGEFKMTDPDEVARRWGERKSKPNMN
YDKLSRALRYYYDKNIMTKVHGKRYAYKFDFHGIAQALQPHPTE

Sequence of entity 2 (B), FASTA

>6VG8_2 DNA (5'-D(P*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3') (chains B)
CAGAGGATGTGGCTTC

Sequence of entity 3 (C), FASTA

>6VG8_3 DNA (5'-D(P*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*TP*G)-3') (chains C)
GAAGCCACATCCTCTG

Sequence of entity 4 (D), FASTA

>6VG8_4 Runt-related transcription factor 2 (chains D)
AELVRTDSPNFLCSVLPSHWRCNKTLPVAFKVVALGEVPDGTVVTVMAGNDENYSAELRN
ASAVMKNQVARFNDLRFVGRSGRGKSFTLTITVFTNPPQVATYHRAIKVTVDGPREPRRH
RQK

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…
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…
1FLI DNA-binding domain of fli-1
1X66 Solution structure of the SAM_PNT-domain of the human friend LEUKEMIAINTEGRATION 1…

Browse structure collections

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