2025-10-08 REL PDBe INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID _em_admin.last_update PDBe PDBe 2025-08-07 2025-10-01 2025-10-01 2025-10-08 Not funded Ternary PROTAC-mediated complex of BRD4-BD1/CRBN/DDB1 and JQ1-AcQ bifunctional degrader Peter D Fischer G Arce Solano S Kessler D Cryo-EM DDB1 (DNA Damage-Binding Protein 1) CRBN (Cereblon) BRD4 (bromodomain containing 4) Protein degradation cyclimid PROTACs, 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-54896 consensus EM volume
Consensus map of ternary PROTAC-mediated complex of BRD4-BD1/CRBN/DDB1 and JQ1-AcQ bifunctional degrader
 EMD-54895 focused EM volume
Focus map of ternary PROTAC-mediated complex of BRD4-BD1/CRBN/DDB1 and JQ1-AcQ bifunctional degrader
 9saf FULLOVERLAP EMDB EMD-54690 associated EM volume
Ternary PROTAC-mediated complex of BRD4-BD1/CRBN/DDB1 and JQ1-AcQ bifunctional degrader
 EMDB EMD-54896 consensus EM volume
Consensus map of ternary PROTAC-mediated complex of BRD4-BD1/CRBN/DDB1 and JQ1-AcQ bifunctional degrader
 EMDB EMD-54895 focused EM volume
Focus map of ternary PROTAC-mediated complex of BRD4-BD1/CRBN/DDB1 and JQ1-AcQ bifunctional degrader
 PROTAC-mediated complex of DDB1 (BPB deletion), CRBN and BRD4 BD1 domain PROTAC-mediated complex of DDB1 (BPB deletion), CRBN and BRD4 BD1 domain 0 1 2 3 Homo sapiens 0.015 Ligase sub-complex consisting of DDB1 (BPB deletion) and CRBN 1 1 2 Homo sapiens degradation target BRD4 (BD1 domain) 1 3 Homo sapiens DNA damage-binding protein 1 Homo sapiens 0.09334707799999999
Deletion of beta-propeller B domain and replacement by short linker sequence
1 Trichoplusia ni LEVO MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFIL TAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLE ELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNG VVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGGNGNS GEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGE EVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEK EVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEE IARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPT QGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPK MQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH Q16531 Protein cereblon Homo sapiens 0.050559559 1 Trichoplusia ni LEVO SAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQV IPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAI GRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSW PRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTS LCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGW KFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL Q96SW2 Bromodomain-containing protein 4 Homo sapiens 0.015099379999999999 1 Escherichia coli LEVO SMNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWN AQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEE O60885 ZINC ION 6.5409e-05 1 ZN ~{N}-[(2~{S})-1-[[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]amino]-1-oxidanylidene-propan-2-yl]-9-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,10,12-tetraen-9-yl]ethanoylamino]nonanamide 0.000739327 1 A1JM8 water 1.8015e-05 89 HOH singleParticle particle 0.3 7.5 20.0 HEPES 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid 100.0 NaCl sodium chloride 0.25 TCEP Tris(2-carboxyethyl)phosphine Quantifoil R1.2/1.3 GOLD 300 GLOW DISCHARGE ETHANE 100 277.15 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.8 2.0 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris X 10 FEI FALCON IV (4k x 4k) 3 38923 50.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 2.55 FSC 0.143 CUT-OFF cryoSPARC 158212 PROJECTION MATCHING PROJECTION MATCHING emd_54690.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 Y X Z -31.690529000000002 48.589545999999999 0.026635734 1.0844532 0.749 0.749 0.749 8.0 AUTHOR composite map