2024-10-23 REL RCSB RCSB RCSB 2023-02-08 2023-03-08 2023-03-08 2024-10-23 National Institutes of Health/National Cancer Institute (NIH/NCI) CA262188 United States National Institutes of Health/National Cancer Institute (NIH/NCI) CA066996 United States The Mark Foundation 19-001-ELA United States Cryo-EM structure of DDB1deltaB-DDA1-DCAF16-BRD4(BD2)-MMH2 Ma MW Hunkeler M Jin CY Fischer ES E3 ligase, ubiquitin, degrader, targeted protein degradation, LIGASE Li YD Ma MW Hassan MM Hunkeler M Teng M Puvar K Lumpkin R Sandoval B Jin CY Ficarro SB Wang MY Xu S Groendyke BJ Sigua LH Tavares I Zou C Tsai JM Park PMC Yoon H Majewski FC Marto JA Qi J Nowak RP Donovan KA Slabicki M Gray NS Fischer ES Ebert BL Template-assisted covalent modification of DCAF16 underlies activity of BRD4 molecular glue degraders. Biorxiv US 2023 36824856 doi:10.1101/2023.02.14.528208 2692-8205 8g46 FULLOVERLAP Ternary complex of cullin ring E3 ubiquitin ligase substrate receptor arm (DDB1deltaB-DDA1-DCAF16) in compound-induced complex with bromodomain 2 of BRD4 Ternary complex of cullin ring E3 ubiquitin ligase substrate receptor arm (DDB1deltaB-DDA1-DCAF16) in compound-induced complex with bromodomain 2 of BRD4 0 1 2 3 4 Homo sapiens 0.148 DNA damage-binding protein 1 Homo sapiens 0.096425586 1 Trichoplusia ni LEVO MGSSHHHHHHSAAHIVMVDAYKPTKGGRMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPV KEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIG LRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENV EAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMD GTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQ GQLVTCSGAFKEGSLRIIRNGIGGNGNSGEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSA STQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMV YPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKT KGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVG LFHLGEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSF HTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH Q16531 Q16531 DDB1- and CUL4-associated factor 16 Homo sapiens 0.024547697 1 Trichoplusia ni LEVO GGGRMGPRNPSPDHLSESESEEEENISYLNESSGEEWDSSEEEDSMVPNLSPLESLAWQVKCLLKYSTTWKPLNPNSWLY HAKLLDPSTPVHILREIGLRLSHCSHCVPKLEPIPEWPPLASCGVPPFQKPLTSPSRLSRDHATLNGALQFATKQLSRTL SRATPIPEYLKQIPNSCVSGCCCGWLTKTVKETTRTEPINTTYSYTDFQKAVNKLLTASL Q9NXF7 Bromodomain-containing protein 4 Homo sapiens 0.014899108999999999 1 Escherichia coli LEVO GKDVPDSQQHPAPEKSSKVSEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEARE YRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDE O60885 DET1- and DDB1-associated protein 1 Homo sapiens 0.012183646 1 Trichoplusia ni LEVO GGGRMADFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLHQQWDKKNAAKKRDQEQ VELEGESSAPPRKVARTDSPDMHEDT Q9BW61 ZINC ION 6.5409e-05 1 ZN tert-butyl [(6S,10P)-4-{4-[(ethanesulfonyl)amino]phenyl}-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetate 0.000529675 1 YK3 water 1.8015e-05 110 HOH singleParticle particle 1.25 7.4 50.0 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid 200.0 NaCl sodium chloride 0.011 Lauryl Maltose Neopentyl Glycol 2.0 tris(2-carboxyethyl)phosphine
50 mM HEPES pH 7.4, 200 mM NaCl, 2 mM TCEP, 0.011% LMNG
 UltrAuFoil R0./1 GOLD 300 GOLD HOLEY 40.0 GLOW DISCHARGE AIR 3.9e-05
20 mA
 ETHANE 90 283 LEICA EM GP
detergent added directly before grid application.
The ternary complex was incubated at RT for 30 min before polishing on through size exclusion chromatography. The purified DCAF16 complex was incubated with an extra 1.2x molar excess of purified BRD4BD2 for 30 minutes at 4 degree C before grid preparation.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.8 2.0 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 1 17118 2.3 50.27 1 14452363
built de novo
 3 C1 FOURIER SPACE 2.2 FSC 0.143 CUT-OFF cryoSPARC 3.3.2 1433050 MAXIMUM LIKELIHOOD cryoSPARC 3.3.2 MAXIMUM LIKELIHOOD cryoSPARC 3.3.2 8 600000.0 cryoSPARC 3.3.2
3D variability followed by clustering in cryoSPARC
 emd_29714.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 265.599 265.599 265.599 90.0 90.0 90.0 X Y Z -2.0747068 3.0200558 -0.00020515308 0.070798434 0.88533 0.88533 0.88533 0.463 AUTHOR main map 6VIX PDB experimental model
for BRD4(BD2)
 6Q0R PDB experimental model
for DDB1 and DDA1
 OTHER
refinement in both real and Fourier space
74.0 emd_29714_msk_1.map emd_29714_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 265.599 265.599 265.599 90.0 90.0 90.0 X Y Z -0.0017866027 2.1165109 0.0008360263 0.020499496 0.88533 0.88533 0.88533 AUTHOR map post-processed with deepEMhancer emd_29714_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 265.599 265.599 265.599 90.0 90.0 90.0 X Y Z -0.4429904 0.9234204 0.000060620714 0.032962874 0.88533 0.88533 0.88533 AUTHOR half map A emd_29714_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 265.599 265.599 265.599 90.0 90.0 90.0 X Y Z -0.4633597 0.88466614 0.000057885736 0.03289616 0.88533 0.88533 0.88533 AUTHOR half map B