DDB1-CRBN with Ikaros(ZF2) and DEG-47: focused map submission

2026-03-25 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 RCSB RCSB 2025-05-28 2025-11-19 2025-11-19 2026-03-25 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM143805 United States DDB1-CRBN with Ikaros(ZF2) and DEG-47: focused map submission Rizvi Z Lander GC E3 ligases, Cullin RING Ligase, CRL4, Cereblon, CRBN, molecular glues, IMiDs, LIGASE, Ikaros Dippon VN Rizvi Z Choudhry AE Chung CW Alkuraya IF Xu W Tao XB Jurewicz AJ Schneck JL Chen W Curnutt NM Kabir F Chan KH Queisser MA Musetti C Dai H Lander GC Benowitz AB Woo CM Identification of an allosteric site on the E3 ligase adapter cereblon. Nature UK 651 482 490 2026 41565821 doi:10.1038/s41586-025-09994-w 1476-4687 0006 NATUAS EMD-70865 consensus EM volume

Raw consensus map of DDB1-CRBN with Ikaros(ZF2) and DEG47

EMD-70867 other EM volume

DDB1-CRBN with Ikaros(ZF2) and DEG-47: composite map and model submission

EMDB EMD-70866 associated EM volume

constituent EM map of DDB1-CRBN with Ikaros(ZF2) and DEG47: focus refined on CRBN

EMDB EMD-70865 consensus EM volume

Raw consensus map of DDB1-CRBN with Ikaros(ZF2) and DEG47

EMDB EMD-70867 other EM volume

DDB1-CRBN with Ikaros(ZF2) and DEG-47: composite map and model submission

DDB1(BPB deleted)-CRBN complex with ikaros ZF2-3 and DEG-47 was incubauted for 30 minutes and then plunge frozen over 1.2/1.3 UltrAufoil DDB1(BPB deleted)-CRBN complex with ikaros ZF2-3 and DEG-47 was incubauted for 30 minutes and then plunge frozen over 1.2/1.3 UltrAufoil 0 1 2 3 Homo sapiens 0.15127264 DNA damage binding protein 1 (DDB1) Homo sapiens

The BPB domain is truncated (396-705 truncation with addition of a GNGNSG linker between BPA and BPC) from DDB1 and co-expressed with Cereblon (CRBN) in SF9 expression system.

Spodoptera aff. frugiperda 1 BOLD-2017 LEVO MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGGNGNSGEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH Q16531 Cereblon (CRBN) Homo sapiens

6X His tag at N-terminus

Spodoptera aff. frugiperda 1 BOLD-2017 LEVO MHHHHHHMAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL Q96SW2 Ikaros (ZF2-3) Homo sapiens

tag less

Escherichia coli BL21(DE3) LEVO TGERPFQCNQCGASFTQKGNLLRHIKLHSGEKPFKCHLCNYACRRRDALTGHLRTHS Q13422 singleParticle particle 0.5 7.0 10.0 C8H18N2O4S HEPES 240.0 NaCl Sodium Chloride 3.0 C9H15O6P TCEP

10mM HEPES, 240mM NaCl, 3mM TCEP

UltrAuFoil R1.2/1.3 GOLD 300 GOLD HOLEY 100.10000000000001 PLASMA CLEANING 12 OTHER 0.0239980266 ETHANE 95 277.15 HOMEMADE PLUNGER

The protein complex with ikaros ZF2-3 was incubated with IMiD DEG-47 and was incubated at 1:2:13 for 30 minutes and then frozen on 1.2/1.3 Au grids

FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 0.8 1.2 19000.0 189189.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 70.0 77.0 TFS FALCON 4i (4k x 4k) 4096 4096 1 4915 4.08 50.0 1 3488921 cryoSPARC 4.6.2 PHASE FLIPPING ONLY AB INITIO RECONSTRUCTION 1 C1 FOURIER SPACE 2.96 FSC 0.143 CUT-OFF cryoSPARC 4.6.2 412326 MAXIMUM LIKELIHOOD cryoSPARC 4.6.2

Ab initio reconstruction, heterogeneous refinement, and homogeneous refinement

MAXIMUM LIKELIHOOD cryoSPARC 4.6.2

Non-uniform refinement

6 cryoSPARC 4.6.2 emd_70866.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 222.0 222.0 222.0 90.0 90.0 90.0 X Y Z -1.3406671 2.0605018 -0.00023054652 0.023370286 0.74 0.74 0.74 0.117 AUTHOR ::::EMDATABANK.org::::EMD-70866:::: 8d7z A 1-1148 PDB experimental model

396-705 residues are truncated in construct as well as structure sequence.

8d7z B 46-427 PDB experimental model

1-46 residues are not observed in EM density

8d7z C 144-169 PDB experimental model

140-144 and 170-196 residues are not observed in the EM density but they were in construct.

RIGID BODY FIT RECIPROCAL 97.799999999999997 emd_70866_msk_1.map emd_70866_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 222.0 222.0 222.0 90.0 90.0 90.0 X Y Z -0.2808047 0.5622941 -0.00023054649 0.008253712 0.74 0.74 0.74 AUTHOR ::::EMDATABANK.org::::EMD-70866:::: emd_70866_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 222.0 222.0 222.0 90.0 90.0 90.0 X Y Z -0.31886646 0.5894983 0.00013661626 0.024388077 0.74 0.74 0.74 AUTHOR ::::EMDATABANK.org::::EMD-70866:::: emd_70866_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 222.0 222.0 222.0 90.0 90.0 90.0 X Y Z -0.28425574 0.61350995 0.00013560716 0.024285294 0.74 0.74 0.74 AUTHOR ::::EMDATABANK.org::::EMD-70866::::