Ternary PROTAC-mediated complex consisting of Cereblon, DDB1 and BRD4-BD1, non-covalently linked by JQ1-AcN

2025-10-29 REL PDBe INITIAL_RELEASE REPOSITORY PDBe PDBe 2025-08-07 2025-10-29 2025-10-29 2025-10-29 Not funded Ternary PROTAC-mediated complex consisting of Cereblon, DDB1 and BRD4-BD1, non-covalently linked by JQ1-AcN Fischer G Peter D Arce-Solano S Kessler D ternary complex, PROTAC, cereblon, LIGASE Zhu Q Fischer G Cheng SS Payne NC Peter D Mody AC Arce-Solano S Shen D Lin Z Mazitschek R Kessler D Woo CM Enzyme-Activated Sugar-Coated Bifunctional Degraders. J.Am.Chem.Soc. US 147 34672 34680 2025 40937862 doi:10.1021/jacs.5c09843 1520-5126 JACSAT EMD-54890 consensus EM volume EMD-54891 focused EM volume 9sai FULLOVERLAP EMDB EMD-54691 associated EM volume

EMDB EMD-54890 consensus EM volume EMDB EMD-54891 focused EM volume Ternary PROTAC-mediated complex consisting of Cereblon, DDB1 and BRD4-BD1, non-covalently linked by JQ1-AcN Ternary PROTAC-mediated complex consisting of Cereblon, DDB1 and BRD4-BD1, non-covalently linked by JQ1-AcN 0 1 2 3 Homo sapiens Protein cereblon Homo sapiens 0.050559559 1 unidentified baculovirus LEVO SAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQV IPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAI GRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSW PRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTS LCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGW KFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL Q96SW2 DNA damage-binding protein 1 Homo sapiens 0.09334707799999999

beta-propeller B removed,beta-propeller B removed,beta-propeller B removed,beta-propeller B removed,beta-propeller B removed,beta-propeller B removed,beta-propeller B removed,beta-propeller B removed

1 unidentified baculovirus LEVO MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFIL TAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLE ELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNG VVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGGNGNS GEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGE EVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEK EVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEE IARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPT QGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPK MQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH Q16531 Q16531 Bromodomain-containing protein 4 Homo sapiens 0.015099379999999999 1 Escherichia coli LEVO SMNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWN AQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEE O60885 ZINC ION 6.5409e-05 1 ZN N-[(2S)-1-[[(3S)-2,5-bis(oxidanylidene)pyrrolidin-3-yl]amino]-1-oxidanylidene-propan-2-yl]-9-[2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]nonanamide 0.0007232849999999999 1 A1JM3 singleParticle particle 0.3 7.5 20.0 HEPES 100.0 NaCl 0.25 TCEP

20 mM HEPES, 100 mM NaCl, 0.25 mM TCEP, pH: 7.5

UltrAuFoil R1.2/1.3 GOLD 300 GOLD HOLEY GLOW DISCHARGE 30

QF-1.2/1.3-3C AuFoil

ETHANE 95 277 FEI VITROBOT MARK IV

complex purified via size exclusion chromatography

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.8 2.0 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris X 10 TFS FALCON 4i (4k x 4k) 3 21670 40.0 1 cryoSPARC PHASE FLIPPING AND AMPLITUDE CORRECTION

ab-initio reconstruction (cryoSPARC)

2.66 FSC 0.143 CUT-OFF cryoSPARC 184507 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_54691.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 287.616 287.616 287.616 90.0 90.0 90.0 Z Y X -50.598469999999999 63.123750000000001 0.008577075 1.197289 0.749 0.749 0.749 10.0 AUTHOR ::::EMDATABANK.org::::EMD-54691:::: composite map 3mxf A PDB experimental model 5fqd A PDB experimental model 5fqd B PDB experimental model FLEXIBLE FIT REAL 94.0 emd_54691_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 287.616 287.616 287.616 90.0 90.0 90.0 X Y Z -0.5527246 0.73944974 0.000035008343 0.010851733 0.749 0.749 0.749 AUTHOR ::::EMDATABANK.org::::EMD-54691:::: focussed map emd_54691_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 287.616 287.616 287.616 90.0 90.0 90.0 X Y Z -0.2729038 0.44297352 -0.00022872067 0.009785281 0.749 0.749 0.749 AUTHOR ::::EMDATABANK.org::::EMD-54691:::: full non-focussed map emd_54691_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 287.616 287.616 287.616 90.0 90.0 90.0 X Y Z -0.9845538 0.8965203 -0.00005765719 0.10423087 0.749 0.749 0.749 AUTHOR ::::EMDATABANK.org::::EMD-54691:::: half map A of full non-focussed map emd_54691_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 287.616 287.616 287.616 90.0 90.0 90.0 X Y Z -0.9126012 0.94390625 -0.00005987514 0.10439201 0.749 0.749 0.749 AUTHOR ::::EMDATABANK.org::::EMD-54691:::: half map B of full non-focussed map