2025-11-05 REL RCSB 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 RCSB RCSB 2025-08-12 2025-10-15 2025-10-15 2025-11-05 Other private Cryo-EM structure of ternary complex BCL6-CRBN-DDB1 with BCL6-760 (LDD, local refined) Zhu J Fang W Pagarigan B Cereblon, BCL6, LDD, degrader, E3, LIGASE Shunatona HP Holmberg Douglas N Rhodes J Thomas W Da Silva D Gamez J Groza M Christoforou A Zhu J Johnson S Dodd D Huang D Griffin J Miseo G Whitefield B Weiss D Rader J Kuzu E Leisten J Del Rosario J Shi L Matyskiela M Chamberlain PP Belmont P Alexander M Zapf CW Groocock L Mortensen DS Discovery of Potent and Selective BCL6 Ligand-Directed Degrader (LDD), BCL6-760. J.Med.Chem. US 68 21502 21519 2025 41055242 doi:10.1021/acs.jmedchem.5c01645 0022-2623 0151 JMCMAR 9q03 FULLOVERLAP EMDB EMD-72086 associated EM volume
Cryo-EM structure of ternary complex BCL6-CRBN-DDB1 with BCL6-760 (LDD, local refined)
 ternary complex of BCL6-CRBN-DDB1 with an LDD BCL6-760 ternary complex of BCL6-CRBN-DDB1 with an LDD BCL6-760 0 1 2
BCL6 BTB domain and CRBN/DDB1 was mixed with BCL6-760 in 1:1:1 ratio
Homo sapiens 0.162 B-cell lymphoma 6 protein Homo sapiens 0.016431863 2 Escherichia coli BL21(DE3) LEVO GSLDYKDDDDKENLYFQGADSCIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTDQLK CNLSVINLDPEINPEGFCILLDFMYTSRLNLREGNIMAVMATAMYLQMEHVVDTCRKFIKASE P41182 Protein cereblon Homo sapiens 0.05358198399999999 1 Spodoptera frugiperda LEVO MSYYHHHHHHDYDIPTTGLVPRGSMMAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPT SHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQF GTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSR EDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLR IQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPS TEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL Q96SW2 ZINC ION 6.5409e-05 1 ZN (3R)-3-(6-{4-[(5-chloro-4-{[3-(3-hydroxy-3-methylbutyl)-1-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-5-yl]amino}pyrimidin-2-yl)(methyl)amino]piperidin-1-yl}-1-methyl-1H-indazol-3-yl)piperidine-2,6-dione 0.000715244 1 A1CM7 singleParticle particle 4.0 7.0 20.0 (2-(4-(2-hydroxyethyl)piperazin-1-yl)ethanesulfonic acid) 200.0 NaCl sodium chloride 1.0 tris(2-carboxyethyl)phosphine 0.25 Dimethyl sulfoxide 0.001 Lauryl Maltose Neopentyl Glycol Quantifoil R1.2/1.3 GOLD 300 GOLD HOLEY GLOW DISCHARGE ETHANE 100 278 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.2 1.8 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS FALCON 4i (4k x 4k) 1 10236 3.16 35.18 1 15859703 cryoSPARC PHASE FLIPPING AND AMPLITUDE CORRECTION 9DQD 1 C1 FOURIER SPACE 3.15 FSC 0.143 CUT-OFF cryoSPARC 112568 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD 2 110000.0 cryoSPARC emd_72086.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 241.92 241.92 241.92 90.0 90.0 90.0 X Y Z -0.114134364 0.25040168 -0.00056750077 0.0043707187 0.945 0.945 0.945 0.0381 AUTHOR pdb_00009dqd PDB experimental model pdb_00005x9o PDB experimental model RIGID BODY FIT REAL emd_72086_msk_1.map emd_72086_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 241.92 241.92 241.92 90.0 90.0 90.0 X Y Z -0.14356388 0.2748176 -0.000104784354 0.014693793 0.945 0.945 0.945 AUTHOR emd_72086_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 241.92 241.92 241.92 90.0 90.0 90.0 X Y Z -0.15481618 0.2916298 -0.00011168655 0.014556465 0.945 0.945 0.945 AUTHOR