2024-03-13 REL PDBe PDBe PDBe 2023-04-20 2023-05-17 2023-05-17 2024-03-13 H2020 Marie Curie Actions of the European Commission 101024945 European Union European Research Council (ERC) ERC-2012-StG-311460 European Union Innovative Medicines Initiative 875510 Switzerland Wellcome Trust 223816/Z/21/Z United Kingdom Medical Research Council (MRC, United Kingdom) 4050845509 United Kingdom European Research Council (ERC) 851478 European Union Austrian Science Fund P32125 Austria Austrian Science Fund P31690 Austria Austrian Science Fund P7909 Austria Ternary structure of intramolecular bivalent glue degrader IBG1 bound to BRD4 and DCAF16:DDB1deltaBPB Cowan AD Sundaramoorthy R Nakasone MA Ciulli A Bromodomain, BET protein, DCAF16, Bivalent glue, Targeted protein degradation, TPD, TRANSCRIPTION Hsia O Hinterndorfer M Cowan AD Iso K Ishida T Sundaramoorthy R Nakasone MA Imrichova H Schatz C Rukavina A Husnjak K Wegner M Correa-Saez A Craigon C Casement R Maniaci C Testa A Kaulich M Dikic I Winter GE Ciulli A Targeted protein degradation via intramolecular bivalent glues. Nature UK 627 204 211 2024 38383787 doi:10.1038/s41586-024-07089-6 1476-4687 0006 NATUAS Hsia O Hinterndorfer M Cowan AD Iso K Ishida I Sundaramoorthy R Nakasone MA Imrichova H Schatz C Rukvina A Husnjak K Wegner M Correa-Saez A Craigon C Casement R Maniaci C Testa A Kaulich M Dikic I Winter GE Ciulli A Targeted protein degradation via intramolecular bivalent glues Biorxiv US 2023 doi:10.1101/2023.02.14.528511 2692-8205 Ternary complex of BRD4 tandem bromodomains, compound 1, DCAF16 and DDB1deltaBPB Ternary complex of BRD4 tandem bromodomains, compound 1, DCAF16 and DDB1deltaBPB 0 1 2 3 Homo sapiens 0.118 DCAF16:DDB1deltaBPB E3 receptor:adaptor complex 1 1 2 Homo sapiens DDB1deltaBPB Homo sapiens Trichoplusia ni LEVO MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGGNGNSGEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH Q16531 DCAF16 Homo sapiens Trichoplusia ni LEVO GGMGPRNPSPDHLSESESEEEENISYLNESSGEEWDSSEEEDSMVPNLSPLESLAWQVKCLLKYSTTWKPLNPNSWLYHAKLLDPSTPVHILREIGLRLSHCSHCVPKLEPIPEWPPLASCGVPPFQKPLTSPSRLSRDHATLNGALQFATKQLSRTLSRATPIPEYLKQIPNSCVSGCCCGWLTKTVKETTRTEPINTTYSYTDFQKAVNKLLTASL Q9NXF7 BRD4 Tandem Bromodomains Homo sapiens Trichoplusia ni LEVO GSTNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEETEIMIVQAKGRGRGRKETGTAKPGVSTVPNTTQASTPPQTQTPQPNPPPVQATPHPFPAVTPDLIVQTPVMTVVPPQPLQTPPPVPPQPQPPPAPAPQPVQSHPPIIAATPQPVKTKKGVKRKADTTTPTTIDPIHEPPSLPPEPKTTKLGQRRESSRPVKPPKKDVPDSQQHPAPEKSSKVSEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPD O60885 singleParticle particle 0.8 7.5 20.0 C8H18N2O4S HEPES 50.0 NaCl sodium chloride 0.5 C9H15O6P TCEP Quantifoil R1.2/1.3 GOLD 400 CARBON HOLEY GLOW DISCHARGE
Current 35 mA
 ETHANE 100 277 FEI VITROBOT MARK IV
3.5 uL complex was dispensed onto the grid, allowed to disperse for 10 s, blotted for 3.5 s using blot force 3, then plunged into liquid ethane.
The components were co-incubated then loaded onto a 10/300 Superdex 200 gl column and the fraction corresponding to the complex was collected and concentrated to 0.8 mg/mL
 TFS GLACIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 1.7 3.2 190000.0 190000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS FALCON 4i (4k x 4k) 1 2075 2.0 12.7 1 3.77 FSC 0.143 CUT-OFF cryoSPARC 4.2.1 192014 MAXIMUM LIKELIHOOD cryoSPARC 4.2.1 MAXIMUM LIKELIHOOD cryoSPARC 4.2.1 emd_17172.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 324 324 324 0 0 0 324 324 324 239.76001 239.76001 239.76001 90.0 90.0 90.0 X Y Z -0.9737328 1.2537807 0.0000097455395 0.03627334 0.74 0.74 0.74 0.17 AUTHOR Sharpened map 6UD7 B PDB experimental model 3MXF A PDB experimental model 6DUV A PDB experimental model Other other
DCAF16 model was derived from both colabfold and model-angelo
 emd_17172_msk_1.map emd_17172_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 324 324 324 0 0 0 324 324 324 239.76001 239.76001 239.76001 90.0 90.0 90.0 X Y Z -0.13078353 0.3134077 0.000009745556 0.0117136175 0.74 0.74 0.74 AUTHOR Unsharpened map emd_17172_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 324 324 324 0 0 0 324 324 324 239.76001 239.76001 239.76001 90.0 90.0 90.0 X Y Z -0.3554837 0.4436773 0.00038258126 0.04545815 0.74 0.74 0.74 AUTHOR Half map A emd_17172_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 324 324 324 0 0 0 324 324 324 239.76001 239.76001 239.76001 90.0 90.0 90.0 X Y Z -0.34189263 0.46969467 0.00038594735 0.045297742 0.74 0.74 0.74 AUTHOR Half map B