9SQ5: DDB1deltaB-CRBN-Pomalidomide complex

Cryo-EM structure of the DDB1deltaB-CRBN-Pomalidomide complex bound to IKZF1(ZF1-ZF2-Helix). Determined by electron microscopy at 3.68 Å resolution. Released 17 Jun 2026.

Method: Electron microscopy
Resolution: 3.68 Å
Organism: Homo sapiens
Chains: 3
Atoms: 9,531
Mol. weight: 162.52 kDa
Ligands: Y70, ZN
Released: 17 Jun 2026

Explore 9SQ5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9SQ5 contains 36 α-helices and 94 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 18 helices, 70 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	1
β-strand	17-21	5	2
β-strand	30-35	6	2
β-strand	38-45	8	2
β-strand	48-56	9	2
β-strand	61-67	7	3
β-strand	70	1	4
β-strand	72	1	4
β-strand	76-81	6	3
β-strand	85-94	10	3
β-strand	97-107	11	3
α-helix	114	1
β-strand	115	1	5
α-helix	116	1
β-strand	121-124	4	5
β-strand	130-136	7	5
β-strand	139-144	6	5
β-strand	151	1	3
β-strand	155-158	4	5
β-strand	163-169	7	6
α-helix	170	1
β-strand	177-183	7	6
β-strand	188-196	9	6
β-strand	201-204	4	6
β-strand	211-212	2	6
β-strand	216-221	6	7
β-strand	229-233	5	7
β-strand	237-241	5	7
β-strand	244-248	5	7
α-helix	252-255	4
β-strand	258-263	6	8
β-strand	270-275	6	8
β-strand	279-289	11	8
β-strand	295-307	13	8
α-helix	310-311	2
β-strand	313-317	5	9
β-strand	321-325	5	9
β-strand	331-336	6	9
β-strand	347-353	7	9
β-strand	359-365	7	10
β-strand	374-379	6	10
α-helix	382-384	3
β-strand	386-392	7	10
β-strand	710-716	7	10
β-strand	720-727	8	11
α-helix	728-730	3
β-strand	732-743	12	11
β-strand	749-751	3	11
β-strand	763-765	3	11
α-helix	777-780	4
β-strand	785-795	11	11
β-strand	801-806	6	11
β-strand	811-819	9	12
β-strand	828-835	8	12
β-strand	846-854	9	12
β-strand	857-866	10	12
β-strand	870-876	7	13
β-strand	879-884	6	13
β-strand	887-893	7	13
β-strand	899-906	8	13
β-strand	913-917	5	14
β-strand	920-924	5	14
β-strand	930-936	7	14
β-strand	941-948	8	14
β-strand	954-961	8	15
β-strand	964-969	6	15
β-strand	973-979	7	15
α-helix	986-989	4
β-strand	991	1	14
β-strand	992-999	8	15
β-strand	1004-1009	6	1
β-strand	1025-1032	8	1
β-strand	1037-1042	6	1
α-helix	1045-1059	15
α-helix	1070-1074	5
β-strand	1076-1077	2	16
β-strand	1082-1083	2	16
β-strand	1086	1	15
β-strand	1088-1090	3	1
α-helix	1091-1095	5
α-helix	1096-1098	3
α-helix	1102-1109	8
α-helix	1112	1
β-strand	1113-1115	3	17
β-strand	1121-1123	3	17
α-helix	1124-1125	2
α-helix	1126-1136	11
α-helix	1137-1139	3

Chain B: 17 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	48	1	18
α-helix	52-56	5
α-helix	58-60	3
β-strand	65-66	2	19
α-helix	73-74	2
β-strand	78-83	6	19
α-helix	91-92	2
β-strand	93	1	19
β-strand	96-101	6	19
α-helix	104-114	11
β-strand	119-127	9	19
β-strand	132-149	18	19
β-strand	152-172	21	19
β-strand	178-184	7	19
α-helix	185-186	2
β-strand	188	1	20
α-helix	193-195	3
α-helix	220-231	12
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-261	12
α-helix	262-264	3
α-helix	277-287	11
α-helix	292-300	9
β-strand	303	1	20
α-helix	304-317	14
β-strand	320-323	4	21
β-strand	330-333	4	21
α-helix	334-336	3
β-strand	337	1	22
β-strand	346-350	5	22
β-strand	356-362	7	22
β-strand	368-375	8	22
β-strand	384-391	8	22
β-strand	397-404	8	22
β-strand	410	1	18
β-strand	413-418	6	22
α-helix	419-421	3
β-strand	422-425	4	21

Chain C: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	145-146	2	23
β-strand	153-154	2	23
α-helix	157-167	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A	protein	864	Homo sapiens	Q16531 (AlphaFold model)
Protein cereblon	B	protein	466	Homo sapiens	Q96SW2 (AlphaFold model)
Isoform Ik7 of DNA-binding protein Ikaros	C	protein	111	Homo sapiens	Q13422 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9SQ5_1 DNA damage-binding protein 1 (chains A)
MGSSHHHHHHSAAHIVMVDAYKPTKGGRMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLL
IAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYK
QSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKEL
KAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENV
EAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYL
LGDMEGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQ
LVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRN
GIGGNGNSGEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSA
STQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSL
VSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEF
NGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYK
PMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVG
LFHLGEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQN
RLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDD
GSGMKREATADDLIKVVEELTRIH

Sequence of entity 2 (B), FASTA

>9SQ5_2 Protein cereblon (chains B)
MGSSHHHHHHSAVDENLYFQGGGRMAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQ
DSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQT
LPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVK
VKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSRE
DQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSN
PIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNE
IFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICAS
HIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL

Sequence of entity 3 (C), FASTA

>9SQ5_3 Isoform Ik7 of DNA-binding protein Ikaros (chains C)
MDWSHPQFEKSAVMSGLNDIFEAQKIEWHEGGGGSGGGGDENLYFQGGGRGERPFQCNQC
GASFTQKGNLLRHIKLHSGEKPFKCHLCNYACRRRDALTGHLRTHSVIKEE

Ligands and cofactors

ID	Name	Formula	Copies
Y70	S-Pomalidomide	C13 H11 N3 O4	1
ZN	Zinc ion	Zn	2

Primary citation

Cryo-EM structure of the DDB1deltaB-CRBN-Pomalidomide complex bound to IKZF1(ZF1-ZF2-Helix). Galli, P., Thoma, N.H. To be published.

Other PDB entries of the same protein (UniProt Q16531 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BBG 1.7 Å, Co-crystal structure of human DDB1 bound to fragment UB028671
9EJQ 1.87 Å, Crystal structure of DDB1 in complex with XS381952
9BBI 1.9 Å, Co-crystal structure of human DDB1 bound to fragment UB028669
9BZ0 1.9 Å, Structure of an STK19-containing TC-NER complex
9BBE 2.0 Å, Co-crystal structure of human DDB1 bound to fragment UB028668
9BBH 2.0 Å, Co-crystal structure of human DDB1 bound to fragment UB028670
9FJX 2.0 Å, Crystal structure of human CRBN-DDB1 in complex with Lenalidomide
9ZXN 2.07 Å, DDB1 delta with compound 26
37MF 2.1 Å, Crystal structure of DDB1 in complex with XS445479
9ZXM 2.19 Å, DDB1 delta with compound 6
8G46 2.2 Å, Cryo-EM structure of DDB1deltaB-DDA1-DCAF16-BRD4(BD2)-MMH2
8ZSW 2.25 Å, Crystal Structure of Human DDB1, a Component of the E3 Ubiquitin Ligase Complex

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