Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449;G416A)

2026-02-04 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY RCSB RCSB 2025-03-24 2026-02-04 2026-02-04 2026-02-04 National Institutes of Health/National Cancer Institute (NIH/NCI) R01CA214608 United States Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449;G416A) Park J Hunkeler M Roy Burman SS Fischer ES DDB1, cereblon, mezigdomide, SALL4, LIGASE Slabicki M Park J Nowak RP Roy Burman SS Pellman J Zou C Razumkov H Carreiro J Rastogi S Goldstein A Nagiec MM Donovan KA Che J Hunkeler M Geng Q Hsu CL Lakshminarayan M Shu C Zon RL Kozicka Z Park PMC Tsai JM Yoon H Jones LH Sperling AS Gray NS Fischer ES Ebert BL Expanding the druggable zinc-finger proteome defines properties of drug-induced degradation. Mol.Cell US 85 3184 3201.e14 2025 40845806 doi:10.1016/j.molcel.2025.07.019 1097-2765 2168 MOCEFL EMD-72215 focused EM volume 9nwt FULLOVERLAP EMDB EMD-49893 associated EM volume

EMDB EMD-72215 focused EM volume Ternary complex of DDB1dB:CRBN:mezigdomide:SALL4(392-449;G416A) Ternary complex of DDB1dB:CRBN:mezigdomide:SALL4(392-449;G416A) 0 1 2 3 Homo sapiens Sal-like protein 4 Homo sapiens 0.011507799999999999

StrepII-Avi-TEV-SALL4(392-449;G416A)

1 Trichoplusia ni LEVO MDWSHPQFEKSAVGLNDIFEAQKIEWHEGGGGSGENLYFQGGGRGTDSSLQIHLRSHTGERPFVCSVCAHRFTTKGNLKV HFHRHPQVKANPQLFAEFQDKV Q9UJQ4 DNA damage-binding protein 1 Homo sapiens 0.09603394500000001

His6-TEV-DDB1(1-1140), with residues 396-705 replaced with a GNGNSG linker,His6-TEV-DDB1(1-1140), with residues 396-705 replaced with a GNGNSG linker,His6-TEV-DDB1(1-1140), with residues 396-705 replaced with a GNGNSG linker,His6-TEV-DDB1(1-1140), with residues 396-705 replaced with a GNGNSG linker

1 Trichoplusia ni LEVO MGSSHHHHHHSAVDENLYFQGGGRMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVG MYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLY DGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEA SMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVT LKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLV TCSGAFKEGSLRIIRNGIGGNGNSGEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQA LSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDF ILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHL GEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH Q16531 Q16531 Protein cereblon Homo sapiens 0.055144594

FLAG-Spy-TEV-CRBN(1-442)

1 Trichoplusia ni LEVO MDYKDDDDKSAVDENLYFQGGGRGGSAHIVMVDAYKPTKGGSGMAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQD SKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKD RTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAV QLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNP IDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVH ETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDK VILCL Q96SW2 ZINC ION 6.5409e-05 2 ZN Mezigdomide 0.00056761 1 QFC singleParticle particle 7.4 50.0 C8H18N2O4S/NaOH HEPES/NaOH pH 7.4 150.0 NaCl NaCl 3.0 C9H15O6P TCEP

50 mM HEPES/NaOH pH 7.4, 150 mM NaCl, 3 mM TCEP

Quantifoil R0.6/1 GOLD 300 GOLD HOLEY 50.0 GLOW DISCHARGE 120 AIR 0.039 ETHANE 90 283 LEICA EM GP

UltrAuFoil R 0.6/1 300 mesh grids were glow-discharged for 2 min at 20 mA and 39 Pa, pre-incubated with 4 uL of 10 uM FLAG-IKZF1(140-196;Q146A/G151N) for 1 min, and blotted from behind for 4 s. 4 uL of the sample was then applied to the grid. Grids were vitrified using an EM GP plunge freezer operated at 90% humidity and 10 C with 0 s pre-blot, 4 s blot, and 0 s post-blot..

10 uM His6-DDB1dB:FLAG-Spy-CRBN, 100 uM mezigdomide, and 20 uM StrepII-Avi-SALL4(392-449;G416A) were mixed in dilution buffer (50 mM HEPES/NaOH pH 7.4, 150 mM NaCl, 3 mM TCEP) and incubated for 1 hr. Additional dilution buffer was added to the mixture to achieve final concentrations of 1.6 uM DDB1dB:CRBN, 16.0 uM mezigdomide, and 3.2 uM SALL4(392-449;G416A), and 4 uL of the diluted mixture were applied to the grid.

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.0 2.4 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER HELIUM GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 1 12502 2.8 55.3

One movie was recorded per hole with 25 holes per stage position

1 9479675

Particles were picked using Topaz (v0.2.5) trained on templates from on-the-fly 2D classification

cryoSPARC 4.2.0 PHASE FLIPPING AND AMPLITUDE CORRECTION

Ab-initio reconstruction

C1 FOURIER SPACE 2.7 FSC 0.143 CUT-OFF cryoSPARC 4.2.0

Particles were re-extracted at 0.83 A/pixel, and subsequently processed by reference-based motion correction and global CTF refinement (per-group beam tilt and trefoil). Homogeneous refinement of these processed particles followed by local refinement with a mask encompassing the full particle yielded a final reconstruction at 2.7 A. A local refinement using the CRBN:drug:ZF-focused mask further improved drug and ZF density.

479953 MAXIMUM LIKELIHOOD cryoSPARC 4.2.0 MAXIMUM LIKELIHOOD cryoSPARC 4.2.0 cryoSPARC 4.2.0

Masked 3D variability analysis into 16 classes using a soft mask encompassing the CRBN:drug:ZF portion. Particles from 9 classes with the most defined ZF density were selected for homogeneous refinement, leading to a reconstruction at 3.0 A.

emd_49893.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 336 336 336 0 0 0 336 336 336 278.88 278.88 278.88 90.0 90.0 90.0 X Y Z -0.5200391 0.7972666 -0.00012368862 0.015935669 0.83000004 0.83000004 0.83000004 0.08 AUTHOR ::::EMDATABANK.org::::EMD-49893:::: Main map, auto-sharpened with cryoSPARC 8TNQ A PDB experimental model 8TNQ B PDB experimental model 8U17 C PDB experimental model 8D7Z D PDB experimental model

Sharpened and unsharpened maps processed by cryoSPARC, in addition to maps post-processed with DeepEMhancer (v0.16), were used for model building. A previously-built model of DDB1dB:CRBN:mezigdomide:SALL4(392-449) was fit into the density as individual chains using ChimeraX (v1.6.1). Using the same ligand restraint file described above, the model was relaxed into the density using Rosetta (v3.13) followed by manual adjustment in Coot. The model was prepared for refinement using phenix.ready_set (v1.21-5207) and refined using phenix.real_space_refine (v1.21-5207).

REAL emd_49893_msk_1.map emd_49893_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 336 336 336 0 0 0 336 336 336 278.88 278.88 278.88 90.0 90.0 90.0 X Y Z -0.0018061853 1.8618822 0.000865972 0.021593004 0.83000004 0.83000004 0.83000004 AUTHOR ::::EMDATABANK.org::::EMD-49893:::: Main map, post-processed with DeepEMhancer emd_49893_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 336 336 336 0 0 0 336 336 336 278.88 278.88 278.88 90.0 90.0 90.0 X Y Z -0.0948724 0.20782694 -0.00012368863 0.004468471 0.83000004 0.83000004 0.83000004 AUTHOR ::::EMDATABANK.org::::EMD-49893:::: Main map, unsharpened emd_49893_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 336 336 336 0 0 0 336 336 336 278.88 278.88 278.88 90.0 90.0 90.0 X Y Z -0.12304182 0.22834629 0.000068345864 0.014539318 0.83000004 0.83000004 0.83000004 AUTHOR ::::EMDATABANK.org::::EMD-49893:::: Main map, half-map A emd_49893_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 336 336 336 0 0 0 336 336 336 278.88 278.88 278.88 90.0 90.0 90.0 X Y Z -0.12151503 0.2267147 0.00006789628 0.014570806 0.83000004 0.83000004 0.83000004 AUTHOR ::::EMDATABANK.org::::EMD-49893:::: Main map, half-map B