DDB1-CRBN with CK1 alpha, SB-405483, and DEG-47: composite map and model submission

2026-03-25 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.year _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.year _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update COORDINATE_REPLACEMENT AUTHOR Model orientation/position

In the earlier version, the two carbonyl groups of the glutarimide ring of DEG-47 were oriented toward the right within the Tri-Trp pocket. In the revised version, the ligand has been flipped such that these carbonyls now face toward the left within the Tri-Trp pocket.

STRUCTURE_SUMMARY atom_site em_admin pdbx_contact_author pdbx_struct_conn_angle pdbx_struct_sheet_hbond pdbx_validate_close_contact pdbx_validate_polymer_linkage pdbx_validate_rmsd_angle pdbx_validate_torsion refine refine_ls_restr struct_conf struct_conn struct_mon_prot_cis struct_sheet struct_sheet_order struct_sheet_range _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _em_admin.last_update _pdbx_struct_conn_angle.value _pdbx_validate_polymer_linkage.dist _struct_conn.pdbx_dist_value _struct_mon_prot_cis.pdbx_omega_angle EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.name _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.name _em_admin.last_update DATABASE_REFERENCES citation em_admin _citation.journal_volume _citation.page_first _citation.page_last _em_admin.last_update EXPERIMENTAL_SUMMARY citation em_admin _citation.journal_volume _citation.page_first _citation.page_last _em_admin.last_update RCSB RCSB 2025-05-27 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 CK1 alpha, SB-405483, and DEG-47: composite map and model submission Rizvi Z Lander GC E3 ligases, Cullin RING Ligase, CRL4, Cereblon, CRBN, molecular glues, IMiDs, LIGASE 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-70827 consensus EM volume

Raw consensus map of DDB1-CRBN with CK1a, SB405483, and DEG-47. Non uniform refinement

EMD-70835 focused EM volume

Constitutent EM map: Focused refinement on CRBN

EMD-70836 focused EM volume

Constitutent EM map: Focused refinement on CK1a

9oty FULLOVERLAP EMDB EMD-70827 consensus EM volume

Raw consensus map of DDB1-CRBN with CK1a, SB405483, and DEG-47. Non uniform refinement

EMDB EMD-70835 focused EM volume

Constitutent EM map: Focused refinement on CRBN

EMDB EMD-70836 focused EM volume

Constitutent EM map: Focused refinement on CK1a

EMDB EMD-70862 associated EM volume

DDB1-CRBN with CK1 alpha, SB-405483, and DEG-47: composite map and model submission

DDB1(BPB deleted)-CRBN complex with Casein kinase 1 alpha, SB-405483, and DEG-47 DDB1(BPB deleted)-CRBN complex with Casein kinase 1 alpha, SB-405483, and DEG-47 0 1 2 3

The protein complex was incubated with CK1a, IMiD DEG-47, and allosteric binder SB-405483, and the mixture was incubated at 1:2:13:20 for 30 minutes and then frozen on 1.2/1.3 Au grids

Homo sapiens 0.18366303 DNA damage-binding protein 1 Homo sapiens 0.093061852 1 Spodoptera aff. frugiperda 1 BOLD-2017 LEVO MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFIL TAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLE ELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNG VVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRLHIRTVPLY ESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHT FEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNG KLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVE ILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIG LVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGS GMKREATADDLIKVVEELTRIHWSHPQFEK Q16531 Q16531 Protein cereblon Homo sapiens 0.043978617 1 Spodoptera aff. frugiperda 1 BOLD-2017 LEVO IINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAY SNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKC QIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVA ACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKA CNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIP Q96SW2 Casein kinase I isoform alpha Homo sapiens 0.034682211000000004 1 Spodoptera aff. frugiperda 1 BOLD-2017 LEVO EFIVGGKYKLVRKIGSGSFGDIYLAINITNGEEVAVKLESQKARHPQLLYESKLYKILQGGVGIPHIRWYGQEKDYNVLV MDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHTKNFIHRDIKPDNFLMGIGRHCNKLFLIDFGLAKKYRDNRT RQHIPYREDKNLTGTARYASINAHLGIEQSRRDDMESLGYVLMYFNRTSLPWQGLKAATKKQKYEKISEKKMSTPVEVLC KGFPAEFAMYLNYCRGLRFEEAPDYMYLRQLFRILFRTLNHQYDYTFDWTMLKQ P48729 2.7.11.1 ZINC ION 6.5409e-05 1 ZN N-{2-[(3R)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide 0.000363367 1 A1CEH N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea 0.000360366 1 A1CEG 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 was incubated with CK1a, IMiD DEG-47, and allosteric binder SB-405483, and the mixture was incubated at 1:2:13:20 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 190000.0 189189.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 70.0 77.0 TFS FALCON 4i (4k x 4k) 4096 4096 2 5691 4.08 50.0 1 3492611 cryoSPARC 4.6.2 PHASE FLIPPING ONLY AB INITIO RECONSTRUCTION 2 C1 FOURIER SPACE 3.0 FSC 0.143 CUT-OFF cryoSPARC 4.6.2 328293 MAXIMUM LIKELIHOOD cryoSPARC 4.6.2

Ab initio reconstruction, heterogeneous refinement, and homogeneous refinement

MAXIMUM LIKELIHOOD cryoSPARC 4.6.2

Non uniform refinement

6 emd_70862.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 -0.12864304 0.4951277 0.0015025148 0.011231561 0.74 0.74 0.74 0.0346 AUTHOR ::::EMDATABANK.org::::EMD-70862:::: A 1-1148 Other experimental model

The initial model was coming from crystal structure model from this study mentioned in citation

B 46-427 Other experimental model

The initial model was coming from crystal structure model from this study mentioned in citation

5fqd C 10-299 PDB experimental model

CK1a model was taken from published structure 5fqd

RIGID BODY FIT RECIPROCAL 102.599999999999994