3WTX: Runt-related transcription factor 1

Crystal structure of the complex comprised of ETS1(Y329A), RUNX1, CBFBETA, and the tcralpha gene enhancer DNA. Determined by X-ray diffraction at 2.8 Å resolution. Released 13 Aug 2014.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Mus musculus, Homo sapiens
Chains: 10
Atoms: 6,940
Mol. weight: 135.8 kDa
Released: 13 Aug 2014

Explore 3WTX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3WTX contains 23 α-helices and 48 β-strands across 6 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: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	62-64	3	1
β-strand	70-73	4	1
β-strand	78-80	3	2
α-helix	83-85	3
β-strand	90-93	4	1
β-strand	102-106	5	3
β-strand	117-118	2	4
β-strand	121-123	3	3
β-strand	124	1	1
β-strand	128-130	3	1
β-strand	135-136	2	4
β-strand	148-152	5	3
β-strand	158-162	5	3
β-strand	167-169	3	2

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-14	7
α-helix	16-19	4
β-strand	25-29	5	3
α-helix	37-49	13
β-strand	52-57	6	3
β-strand	62-67	6	3
β-strand	86-87	2	3
β-strand	95-103	9	3
β-strand	107-114	8	3
β-strand	120-127	8	3
α-helix	129-138	10

Chain C: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	337-345	9
α-helix	348-352	5
β-strand	355-356	2	5
β-strand	362-364	3	5
α-helix	368-379	12
α-helix	386-394	9
α-helix	396-399	4
β-strand	402-404	3	5
β-strand	411-414	4	5
α-helix	418-422	5
α-helix	426-432	7

Chain F: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	62-64	3	6
β-strand	70-73	4	6
α-helix	74-76	3
β-strand	78-80	3	7
α-helix	83-85	3
β-strand	90-93	4	6
β-strand	102-108	7	8
β-strand	117-118	2	9
β-strand	121-123	3	8
β-strand	124-125	2	6
β-strand	128-130	3	6
β-strand	135-136	2	9
β-strand	146-152	7	8
β-strand	158-166	9	8
β-strand	167-169	3	7

Chain G: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-12	5
α-helix	16-22	7
β-strand	25-29	5	8
α-helix	37-50	14
β-strand	52-57	6	8
β-strand	62-67	6	8
β-strand	86-87	2	8
β-strand	95-103	9	8
β-strand	107-114	8	8
β-strand	120-127	8	8
α-helix	129-137	9

Chain H: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	337-346	10
α-helix	348-350	3
β-strand	355-356	2	10
β-strand	363-364	2	10
α-helix	368-378	11
α-helix	386-394	9
β-strand	404	1	10
β-strand	411-412	2	10
α-helix	428-431	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Runt-related transcription factor 1	A, F	protein	204	Mus musculus	Q03347 (AlphaFold model)
Core-binding factor subunit beta	B, G	protein	142	Mus musculus	Q08024 (AlphaFold model)
Protein C-ets-1	C, H	protein	166	Homo sapiens	P14921 (AlphaFold model)
DNA (5'-d(gpapapgpcpcpapcpaptpcpcptpcp*t)-3')	D, I	DNA	15
DNA (5'-d(apgpapgpgpaptpgptpgpgpcptptp*c)-3')	E, J	DNA	15

Sequence of entity 1 (A, F), FASTA

>3WTX_1 Runt-related transcription factor 1 (chains A, F)
GELVRTDSPNFLCSVLPTHWRCNKTLPIAFKVVAKGDVPDGTLVTVMAGNDENYSAELRN
ATAAMKNQVARFNDLRFVGRSGRGKSFTLTITVFTNPPQVATYHRAIKITVDGPREPRRH
RQKLDDQTKPGSLSFSERLSELEQLRRTAMRVSPHHPAPTPNPRASLNHSTAFNPQPQSQ
MQDARQIQPSPPWSYDQSYQYLGS

Sequence of entity 2 (B, G), FASTA

>3WTX_2 Core-binding factor subunit beta (chains B, G)
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQTRFQNACRDGRSEIAFVAT
GTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLHRLD
GMGCLEFDEERAQQEDALAQQA

Sequence of entity 3 (C, H), FASTA

>3WTX_3 Protein C-ets-1 (chains C, H)
SLQRVPSYDSFDSEDYPAALPNHKPKGTFKDYVRDRADLNKDKPVIPAAALAGATGSGPI
QLWQFLLELLTDKSCQSFISWTGDGWEFKLSDPDEVARRWGKRKNKPKMNYEKLSRGLRY
YYDKNIIHKTAGKRYVYRFVCDLQSLLGYTPEELHAMLDVKPDADE

Sequence of entity 4 (D, I), FASTA

>3WTX_4 DNA (5'-D(*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*T)-3') (chains D, I)
GAAGCCACATCCTCT

Sequence of entity 5 (E, J), FASTA

>3WTX_5 DNA (5'-D(*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3') (chains E, J)
AGAGGATGTGGCTTC

Primary citation

A novel allosteric mechanism on protein-DNA interactions underlying the phosphorylation-dependent regulation of Ets1 target gene expressions. Shiina, M., Hamada, K., Inoue-Bungo, T. et al. J Mol Biol (2015) 427:1655-1669. DOI 10.1016/j.jmb.2014.07.020 · PubMed

Other PDB entries of the same protein (UniProt Q03347 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1EAQ 1.25 Å, The RUNX1 Runt domain at 1.25A resolution: A structural switch and specifically bound…
1EAO 1.4 Å, THE RUNX1 Runt domain at 1.4A resolution: a structural switch and specifically bound…
1EAN 1.7 Å, THE RUNX1 Runt domain at 1.70A resolution: A structural switch and specifically bound…
4L18 2.3 Å, Crystal structure of Runx1 and Ets1 bound to TCR alpha promoter (crystal form 3)
3WTS 2.35 Å, Crystal structure of the complex comprised of ETS1, RUNX1, CBFBETA, and the tcralpha…
3WTT 2.35 Å, Crystal structure of the complex comprised of phosphorylated ETS1, RUNX1, CBFBETA, and…
3WU1 2.4 Å, Crystal structure of the ETS1-RUNX1-DNA ternary complex
4L0Y 2.5 Å, Crystal structure of Runx1 and Ets1 bound to TCR alpha promoter (crystal form 1)
2J6W 2.6 Å, R164N mutant of the RUNX1 Runt domain
1HJC 2.65 Å, Crystal structure of runx-1/AML1/CBFALPHA runt domain bound to a DNA fragment from the…
3WTU 2.7 Å, Crystal structure of the complex comprised of ETS1 (V170A), RUNX1, CBFBETA, and the…
3WTV 2.7 Å, Crystal structure of the complex comprised of ETS1(V170G), RUNX1, CBFBETA, and the…

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