9Q22: Ternary complex Helios-ZF2:I-19:CRBN:DDB1

Crystal structure of ternary complex Helios-ZF2:I-19:CRBN:DDB1. Determined by X-ray diffraction at 3.41 Å resolution. Released 1 Oct 2025.

Method: X-ray diffraction
Resolution: 3.41 Å
Organism: Homo sapiens
Chains: 3
Atoms: 9,431
Mol. weight: 148.75 kDa
Ligands: ZN, A1CNP
Released: 1 Oct 2025

Explore 9Q22 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Q22 contains 31 α-helices and 90 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: 13 helices, 65 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	38-44	7	2
β-strand	49-56	8	2
β-strand	61-67	7	3
β-strand	76-81	6	3
β-strand	85-94	10	3
β-strand	97-107	11	3
β-strand	115	1	4
β-strand	121-124	4	5
β-strand	130-134	5	5
β-strand	136	1	4
β-strand	139-144	6	5
β-strand	155-158	4	5
β-strand	163-169	7	6
α-helix	170	1
β-strand	177-184	8	6
β-strand	187-196	10	6
β-strand	201-204	4	6
β-strand	218-221	4	7
α-helix	222-223	2
β-strand	229-232	4	7
β-strand	237-241	5	7
β-strand	244-248	5	7
α-helix	251-255	5
β-strand	258-263	6	8
β-strand	270-275	6	8
β-strand	279-288	10	8
β-strand	296-307	12	8
β-strand	311-318	8	9
β-strand	321-326	6	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
β-strand	732-743	12	11
α-helix	744	1
β-strand	749-751	3	11
β-strand	762-765	4	11
α-helix	766-768	3
β-strand	785-795	11	11
β-strand	801-806	6	11
α-helix	807-808	2
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	929-936	8	14
β-strand	941-949	9	14
β-strand	954-959	6	15
β-strand	964-969	6	15
β-strand	973-978	6	15
β-strand	991	1	14
β-strand	993-999	7	15
β-strand	1004-1009	6	1
β-strand	1025-1032	8	1
β-strand	1037-1042	6	1
α-helix	1045-1061	17
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	1096-1099	4
α-helix	1102-1108	7
α-helix	1127-1137	11

Chain B: 17 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	48	1	17
α-helix	53-56	4
α-helix	58-60	3
β-strand	65-66	2	18
α-helix	73-74	2
β-strand	78-83	6	18
α-helix	91-92	2
β-strand	96-101	6	18
α-helix	104-115	12
β-strand	119-127	9	18
β-strand	132-149	18	18
β-strand	152-172	21	18
β-strand	178-184	7	18
α-helix	185-187	3
β-strand	188	1	19
α-helix	200-205	6
α-helix	220-231	12
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-262	13
α-helix	269-272	4
α-helix	277-286	10
α-helix	292-300	9
β-strand	303	1	19
α-helix	304-317	14
β-strand	320-323	4	20
β-strand	330-333	4	20
α-helix	334-336	3
β-strand	337	1	21
β-strand	341	1	22
β-strand	344	1	22
β-strand	346-350	5	21
β-strand	356-362	7	21
β-strand	368-375	8	21
β-strand	384-391	8	21
β-strand	397-404	8	21
β-strand	410	1	17
β-strand	413-418	6	21
α-helix	419-421	3
β-strand	422-425	4	20

Chain C: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	140-141	2	23
β-strand	148-149	2	23
α-helix	152-159	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A	protein	856	Homo sapiens	Q16531 (AlphaFold model)
Protein cereblon	B	protein	426	Homo sapiens	Q96SW2 (AlphaFold model)
Zinc finger protein Helios	C	protein	31	Homo sapiens	Q9UKS7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9Q22_1 DNA damage-binding protein 1 (chains A)
MHHHHHHVDEENLYFQGGGRMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLE
IYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDI
ITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLE
ELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVI
AVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRL
FMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDS
NEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGGNGNS
GEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSS
VSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKD
PNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASI
NSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEE
IARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFV
NVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKS
VGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREA
TADDLIKVVEELTRIH

Sequence of entity 2 (B), FASTA

>9Q22_2 Protein cereblon (chains B)
MDWSHPQFEKSAVDENLYFQGGGRAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDD
SCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFG
TTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSA
VQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDR
IKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMN
KCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPST
EHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPD
KVILCL

Sequence of entity 3 (C), FASTA

>9Q22_3 Zinc finger protein Helios (chains C)
GSTGERPFHCNQCGASFTQKGNLLRHIKLHS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
A1CNP	(3S)-3-[5-(1-benzyl-4-hydroxypiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl…	C25 H27 N3 O4	1

Primary citation

Application of Weighted Interaction-Fingerprints for Rationalizing Neosubstrate Potency and Selectivity of Cereblon-Based Molecular Glues. Luchini, G., Liu, S., Powers, H.L. et al. J Med Chem (2025) 68:20657-20674. DOI 10.1021/acs.jmedchem.5c01919 · PubMed

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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