Cryo-EM Structure of CRBN:dHTC1:ENL YEATS

2025-11-19 REL RCSB INITIAL_RELEASE REPOSITORY RCSB RCSB 2024-10-04 2025-11-19 2025-11-19 2025-11-19 National Institutes of Health/National Cancer Institute (NIH/NCI) R01CA214608 United States Cryo-EM Structure of CRBN:dHTC1:ENL YEATS Cheong H Hunkeler M Fischer ES Mammalian, ENL YEATS, CRBN, dHTC1, CIP, targeted protein degradation, LIGASE Shaum JB Munoz I Ordono M Steen EA Wenge DV Cheong H Hunkeler M Bilotta EM Rutter Z Barta PA Thornhill AM Milosevich N Hargis LM Janowski J Bishop TR Carter TR da Camara B Hinterndorfer M Dada L He WJ Offensperger F Furihata H Schweber SR Hatton C Wen Y Cravatt BF Engle KM Donovan KA Melillo B Kitamura S Ciulli A Armstrong SA Fischer ES Winter GE Erb MA High-throughput diversification of protein-ligand surfaces to discover chemical inducers of proximity. Biorxiv US 2025 40950085 doi:10.1101/2024.09.30.615685 2692-8205 9dur FULLOVERLAP EMDB EMD-47174 associated EM volume

Ternary complex of dHTC1 induced DDB1dB/CRBN, ENL YEATS complex Ternary complex of dHTC1 induced DDB1dB/CRBN, ENL YEATS complex 0 1 2

ENL YEATS domain bound to full length CRBN bound via degrader dHTC1

0.169 ENL YEATS domain 1 2 Homo sapiens 0.0182 DDB1dB/CRBN 1 1 Homo sapiens 0.151 Protein cereblon Homo sapiens 0.055144594

N terminal FLAG tagged CRBN

1 Trichoplusia ni LEVO MDYKDDDDKSAVDENLYFQGGGRGGSAHIVMVDAYKPTKGGSGMAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQD SKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKD RTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAV QLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNP IDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVH ETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDK VILCL Q96SW2 Protein ENL Homo sapiens 0.018225002

C terminal His tag

1 Escherichia coli B LEVO MDNQCTVQVRLELGHRAQLRKKPTTEGFTHDWMVFVRGPEQCDIQHFVEKVVFWLHDSFPKPRRVCKEPPYKVEESGYAG FIMPIEVHFKNKEEPRKVCFTYDLFLNLEGNPPVNHLRCEKLTFNNPTTEFRYKLLRAGGVMVMPEGAHHHHHH Q03111 ZINC ION 6.5409e-05 1 ZN 2-[3-[2-[4-[[(5~{S})-1,3-bis(oxidanylidene)-2,7-diazaspiro[4.4]nonan-7-yl]sulfonylamino]piperidin-1-yl]ethylcarbamoyl]phenyl]-~{N}-cyclobutyl-imidazo[1,2-a]pyridine-6-carboxamide 0.000676786 1 A1IQT singleParticle particle 7.4 30.0 C8H18N2O4S HEPES 150.0 NaCl Sodium chloride

30 mM HEPES/NaOH pH7.4, 150 mM NaCl. DMSO concentrations were kept below 2% (v/v)

Quantifoil R0.6/1 GOLD 300 GOLD HOLEY 5.0 GLOW DISCHARGE 120 AIR 0.039 ETHANE 90 283 LEICA EM GP

Grids were vitrified using a Leica EM GP plunge freezer operated at 90% humidity and 10 C. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixturewas applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.

Particles from two grids were merged for this data set. The grids differed in protein concentration. Grid1: DDB1dB/CRBN:dHTC1:ENL YEATS of 1.4, 14, 2.8 uM Grid2: DDB1dB/CRBN:dHTC1:ENL YEATS of 1.6, 16, 3.2 uM

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.8 2.0 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris 10 TFS FALCON 4i (4k x 4k) 2 22883 2.87 52.0 1 9955887 cryoSPARC 4.5.3 PHASE FLIPPING AND AMPLITUDE CORRECTION 2.9 FSC 0.143 CUT-OFF cryoSPARC 4.5.3 185312 MAXIMUM LIKELIHOOD cryoSPARC 4.5.3 MAXIMUM LIKELIHOOD cryoSPARC 4.5.3 12 cryoSPARC 4.5.3 emd_47174.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 235.52 235.52 235.52 90.0 90.0 90.0 X Y Z -0.119131066 0.2203039 0.00018670727 0.004170458 0.92 0.92 0.92 0.03 AUTHOR ::::EMDATABANK.org::::EMD-47174:::: 8tnq B PDB experimental model 6phy A PDB experimental model 119.799999999999997 emd_47174_msk_1.map emd_47174_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 235.52 235.52 235.52 90.0 90.0 90.0 X Y Z -0.0017057669 2.2322912 0.00094029924 0.019339798 0.92 0.92 0.92 AUTHOR ::::EMDATABANK.org::::EMD-47174:::: DeepEMhancer emd_47174_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 235.52 235.52 235.52 90.0 90.0 90.0 X Y Z -0.7317964 0.95720917 0.00018670727 0.013463979 0.92 0.92 0.92 AUTHOR ::::EMDATABANK.org::::EMD-47174:::: emd_47174_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 235.52 235.52 235.52 90.0 90.0 90.0 X Y Z -0.14199382 0.24849427 0.0002349849 0.009308959 0.92 0.92 0.92 AUTHOR ::::EMDATABANK.org::::EMD-47174:::: emd_47174_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 235.52 235.52 235.52 90.0 90.0 90.0 X Y Z -0.13181299 0.24088089 0.00022749648 0.009324441 0.92 0.92 0.92 AUTHOR ::::EMDATABANK.org::::EMD-47174::::