Crystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), in complex with 16mer DNA CAGAGGATGTGGCTTC. Determined by X-ray diffraction at 4.25 Å resolution. Released 25 Nov 2020.
Explore 6VGE in 3D Show helices and sheets RCSB PDB PDBe
6VGE contains 9 α-helices and 28 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 314-321 | 8 | |
| α-helix | 324-326 | 3 | |
| β-strand | 330-332 | 3 | 1 |
| β-strand | 339-341 | 3 | 1 |
| α-helix | 344-355 | 12 | |
| α-helix | 362-375 | 14 | |
| β-strand | 378-380 | 3 | 1 |
| β-strand | 388-390 | 3 | 1 |
| α-helix | 392-395 | 4 |
| 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 | 199 | 1 | 6 |
| β-strand | 200-204 | 5 | 4 |
| β-strand | 209-210 | 2 | 4 |
| β-strand | 213 | 1 | 6 |
| β-strand | 218-220 | 3 | 3 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 8-12 | 5 | |
| α-helix | 16-19 | 4 | |
| β-strand | 25-29 | 5 | 7 |
| α-helix | 37-50 | 14 | |
| β-strand | 52-57 | 6 | 7 |
| β-strand | 63-67 | 5 | 7 |
| β-strand | 94-95 | 2 | 7 |
| β-strand | 102-103 | 2 | 4 |
| β-strand | 106-107 | 2 | 4 |
| β-strand | 108 | 1 | 8 |
| β-strand | 114-115 | 2 | 7 |
| β-strand | 120-123 | 4 | 7 |
| β-strand | 127 | 1 | 8 |
| α-helix | 129-136 | 8 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Transcriptional regulator ERG | A | protein | 128 | Homo sapiens | P11308 (AlphaFold model) |
| DNA (5'-d(p*cp*ap*gp*ap*gp*gp*ap*tp*gp*tp*gp*gp*cp*tp*tp*c)-3') | B | DNA | 16 | Homo sapiens | |
| DNA (5'-d(p*gp*ap*ap*gp*cp*cp*ap*cp*ap*tp*cp*cp*tp*cp*tp*g)-3') | C | DNA | 16 | Homo sapiens | |
| Runt-related transcription factor 2 | D | protein | 177 | Homo sapiens | Q13950 (AlphaFold model) |
| Core-binding factor subunit beta | G | protein | 156 | Homo sapiens | Q13951 (AlphaFold model) |
>6VGE_1 Transcriptional regulator ERG (chains A) GPHMPGSGQIQLWQFLLELLSDSSNSSCITWEGTNGEFKMTDPDEVARRWGERKSKPNMN YDKLSRALRYYYDKNIMTKVHGKRYAYKFDFHGIAQALQPHPPESSLYKYPSDLPYMGSY HAHPQKMN
>6VGE_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
>6VGE_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
>6VGE_4 Runt-related transcription factor 2 (chains D) AELVRTDSPNFLCSVLPSHWRCNKTLPVAFKVVALGEVPDGTVVTVMAGNDENYSAELRN ASAVMKNQVARFNDLRFVGRSGRGKSFTLTITVFTNPPQVATYHRAIKVTVDGPREPRRH RQKLDDSKPSLFSDRLSDLGRIPHPSMRVGVPPQNPRPSLNSAPSPFNPQGQSQITD
>6VGE_5 Core-binding factor subunit beta (chains G) MGSSHHHHHHSQDPMPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQN ACRDGRSEIAFVATGTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGV CVIWKGWIDLQRLDGMGCLEFDEERAQQEDALAQQA
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 P11308 (AlphaFold model), which also has an AlphaFold model), best resolution first:
MolViewer shows 6VGE directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.