Crystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), and mithramycin, in complex with 16mer DNA CAGAGGATGTGGCTTC. Determined by X-ray diffraction at 4.31 Å resolution. Released 25 Nov 2020.
Explore 6VGG in 3D Show helices and sheets RCSB PDB PDBe
6VGG contains 9 α-helices and 32 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 | 332 | 1 | 1 |
| β-strand | 339 | 1 | 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 | 153-155 | 3 | 4 |
| β-strand | 156-157 | 2 | 5 |
| β-strand | 159 | 1 | 6 |
| β-strand | 165 | 1 | 6 |
| β-strand | 168-169 | 2 | 7 |
| β-strand | 172-174 | 3 | 4 |
| β-strand | 175-176 | 2 | 2 |
| β-strand | 179-182 | 4 | 2 |
| β-strand | 186-187 | 2 | 7 |
| β-strand | 199 | 1 | 8 |
| β-strand | 200-201 | 2 | 5 |
| β-strand | 209-210 | 2 | 9 |
| β-strand | 213 | 1 | 8 |
| 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 | 10 |
| α-helix | 37-50 | 14 | |
| β-strand | 52-57 | 6 | 10 |
| β-strand | 63-67 | 5 | 10 |
| β-strand | 94-95 | 2 | 10 |
| β-strand | 102-103 | 2 | 9 |
| β-strand | 106-107 | 2 | 9 |
| β-strand | 108 | 1 | 11 |
| β-strand | 114-115 | 2 | 10 |
| β-strand | 120-123 | 4 | 10 |
| β-strand | 127 | 1 | 11 |
| 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) |
>6VGG_1 Transcriptional regulator ERG (chains A) GPHMPGSGQIQLWQFLLELLSDSSNSSCITWEGTNGEFKMTDPDEVARRWGERKSKPNMN YDKLSRALRYYYDKNIMTKVHGKRYAYKFDFHGIAQALQPHPPESSLYKYPSDLPYMGSY HAHPQKMN
>6VGG_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
>6VGG_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
>6VGG_4 Runt-related transcription factor 2 (chains D) AELVRTDSPNFLCSVLPSHWRCNKTLPVAFKVVALGEVPDGTVVTVMAGNDENYSAELRN ASAVMKNQVARFNDLRFVGRSGRGKSFTLTITVFTNPPQVATYHRAIKVTVDGPREPRRH RQKLDDSKPSLFSDRLSDLGRIPHPSMRVGVPPQNPRPSLNSAPSPFNPQGQSQITD
>6VGG_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:
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