3WTY: Runt-related transcription factor 1
Crystal structure of the complex comprised of ETS1(G333P), RUNX1, CBFBETA, and the tcralpha gene enhancer DNA. Determined by X-ray diffraction at 2.7 Å resolution. Released 13 Aug 2014.
- Method
- X-ray diffraction
- Resolution
- 2.7 Å
- Organisms
- Mus musculus, Homo sapiens
- Chains
- 10
- Atoms
- 7,039
- Mol. weight
- 136.07 kDa
- Released
- 13 Aug 2014
Explore 3WTY in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3WTY contains 28 α-helices and 50 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: 3 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 64 | 1 | 1 |
| β-strand | 70-72 | 3 | 1 |
| α-helix | 73-76 | 4 | |
| β-strand | 78-80 | 3 | 2 |
| α-helix | 83-85 | 3 | |
| β-strand | 90-93 | 4 | 1 |
| β-strand | 102-108 | 7 | 3 |
| β-strand | 109 | 1 | 4 |
| β-strand | 112 | 1 | 4 |
| β-strand | 117-118 | 2 | 5 |
| β-strand | 121-123 | 3 | 3 |
| β-strand | 124-125 | 2 | 1 |
| β-strand | 128-130 | 3 | 1 |
| β-strand | 135-136 | 2 | 5 |
| β-strand | 146-152 | 7 | 3 |
| α-helix | 157 | 1 | |
| β-strand | 158-166 | 9 | 3 |
| β-strand | 167-169 | 3 | 2 |
Chain B: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-13 | 4 | |
| 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 | 1 | 3 |
| β-strand | 94-103 | 10 | 3 |
| β-strand | 106-115 | 10 | 3 |
| β-strand | 120-127 | 8 | 3 |
| α-helix | 129-138 | 10 | |
Chain C: 8 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 323-326 | 4 | |
| α-helix | 337-345 | 9 | |
| α-helix | 348-350 | 3 | |
| β-strand | 354-356 | 3 | 6 |
| β-strand | 362-365 | 4 | 6 |
| α-helix | 368-379 | 12 | |
| α-helix | 386-394 | 9 | |
| α-helix | 396-399 | 4 | |
| β-strand | 402-404 | 3 | 6 |
| β-strand | 411-414 | 4 | 6 |
| 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 | 7 |
| β-strand | 70-73 | 4 | 7 |
| α-helix | 74-76 | 3 | |
| β-strand | 78-80 | 3 | 8 |
| α-helix | 83-85 | 3 | |
| β-strand | 90-93 | 4 | 7 |
| β-strand | 102-108 | 7 | 9 |
| β-strand | 117-118 | 2 | 10 |
| β-strand | 121-123 | 3 | 9 |
| β-strand | 124-125 | 2 | 7 |
| β-strand | 128-130 | 3 | 7 |
| β-strand | 135-136 | 2 | 10 |
| β-strand | 146-152 | 7 | 9 |
| β-strand | 158-166 | 9 | 9 |
| β-strand | 167-169 | 3 | 8 |
Chain G: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-14 | 7 | |
| α-helix | 16-22 | 7 | |
| β-strand | 25-29 | 5 | 9 |
| α-helix | 37-50 | 14 | |
| β-strand | 52-57 | 6 | 9 |
| β-strand | 62-67 | 6 | 9 |
| β-strand | 86-87 | 2 | 9 |
| β-strand | 94-103 | 10 | 9 |
| β-strand | 106-115 | 10 | 9 |
| β-strand | 120-127 | 8 | 9 |
| α-helix | 129-137 | 9 | |
Chain H: 7 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 337-346 | 10 | |
| α-helix | 348-350 | 3 | |
| β-strand | 355-356 | 2 | 11 |
| β-strand | 363-364 | 2 | 11 |
| α-helix | 368-378 | 11 | |
| α-helix | 386-394 | 9 | |
| α-helix | 396-399 | 4 | |
| β-strand | 403-404 | 2 | 11 |
| β-strand | 411-413 | 3 | 11 |
| α-helix | 426-429 | 4 | |
| α-helix | 430-432 | 3 | |
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(*gp*ap*ap*gp*cp*cp*ap*cp*ap*tp*cp*cp*tp*cp*t)-3') | D, I | DNA | 15 | | |
| DNA (5'-d(*ap*gp*ap*gp*gp*ap*tp*gp*tp*gp*gp*cp*tp*tp*c)-3') | E, J | DNA | 15 | | |
Sequence of entity 1 (A, F), FASTA
>3WTY_1 Runt-related transcription factor 1 (chains A, F)
GELVRTDSPNFLCSVLPTHWRCNKTLPIAFKVVAKGDVPDGTLVTVMAGNDENYSAELRN
ATAAMKNQVARFNDLRFVGRSGRGKSFTLTITVFTNPPQVATYHRAIKITVDGPREPRRH
RQKLDDQTKPGSLSFSERLSELEQLRRTAMRVSPHHPAPTPNPRASLNHSTAFNPQPQSQ
MQDARQIQPSPPWSYDQSYQYLGS
Sequence of entity 2 (B, G), FASTA
>3WTY_2 Core-binding factor subunit beta (chains B, G)
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQTRFQNACRDGRSEIAFVAT
GTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLHRLD
GMGCLEFDEERAQQEDALAQQA
Sequence of entity 3 (C, H), FASTA
>3WTY_3 Protein C-ets-1 (chains C, H)
SLQRVPSYDSFDSEDYPAALPNHKPKGTFKDYVRDRADLNKDKPVIPAAALAGYTGSPPI
QLWQFLLELLTDKSCQSFISWTGDGWEFKLSDPDEVARRWGKRKNKPKMNYEKLSRGLRY
YYDKNIIHKTAGKRYVYRFVCDLQSLLGYTPEELHAMLDVKPDADE
Sequence of entity 4 (D, I), FASTA
>3WTY_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
>3WTY_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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