9NWT: DDB1dB:CRBN:mezigdomide:SALL4(392-449;G416A)

Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449;G416A). Determined by electron microscopy at 2.7 Å resolution. Released 4 Feb 2026.

Method: Electron microscopy
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 3
Atoms: 9,655
Mol. weight: 163.38 kDa
Ligands: QFC, ZN
Released: 4 Feb 2026

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

Secondary structure: helices and β-sheets

9NWT contains 38 α-helices and 89 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: 17 helices, 68 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	2
β-strand	15-21	7	3
β-strand	30-35	6	3
β-strand	38-45	8	3
β-strand	48-56	9	3
β-strand	61-67	7	4
β-strand	76-81	6	4
β-strand	85-94	10	4
β-strand	97-107	11	4
α-helix	114	1
β-strand	115	1	5
α-helix	116	1
β-strand	121-124	4	6
β-strand	130-134	5	6
β-strand	136	1	5
β-strand	139-144	6	6
β-strand	155-158	4	6
β-strand	164-169	6	7
α-helix	170	1
β-strand	177-184	8	7
β-strand	187-196	10	7
β-strand	201-204	4	7
β-strand	210-211	2	7
β-strand	218-221	4	8
β-strand	229-232	4	8
β-strand	237-241	5	8
β-strand	244-248	5	8
α-helix	251-253	3
β-strand	258-263	6	9
β-strand	270-275	6	9
β-strand	279-289	11	9
β-strand	295-307	13	9
β-strand	313-318	6	10
β-strand	321-325	5	10
β-strand	331-336	6	10
β-strand	347-353	7	10
β-strand	361-365	5	11
β-strand	374-379	6	11
α-helix	382-384	3
β-strand	386-391	6	11
β-strand	711-716	6	11
β-strand	720-727	8	12
β-strand	732-743	12	12
β-strand	749-751	3	12
α-helix	756-758	3
β-strand	762-765	4	12
β-strand	785-795	11	12
β-strand	801-806	6	12
α-helix	807-808	2
β-strand	811-819	9	13
β-strand	828-835	8	13
β-strand	846-854	9	13
β-strand	857-866	10	13
β-strand	870-876	7	14
β-strand	879-884	6	14
β-strand	887-893	7	14
β-strand	899-906	8	14
β-strand	913-917	5	15
β-strand	920-924	5	15
β-strand	929-936	8	15
β-strand	941-949	9	15
β-strand	954-959	6	16
β-strand	964-969	6	16
β-strand	973-979	7	16
α-helix	986-989	4
β-strand	991	1	15
β-strand	992-999	8	16
β-strand	1004-1009	6	2
β-strand	1025-1032	8	2
β-strand	1037-1042	6	2
α-helix	1045-1058	14
α-helix	1062-1064	3
α-helix	1070-1074	5
β-strand	1076-1078	3	17
β-strand	1081-1083	3	17
β-strand	1086	1	16
β-strand	1088-1090	3	2
α-helix	1091-1095	5
α-helix	1096-1098	3
α-helix	1102-1109	8
β-strand	1113	1	18
α-helix	1122	1
β-strand	1123	1	18
α-helix	1124	1
α-helix	1126-1137	12

Chain B: 19 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	53-56	4
α-helix	58-60	3
β-strand	65-66	2	19
β-strand	78-83	6	19
β-strand	96-101	6	19
α-helix	104-114	11
β-strand	119-123	5	19
β-strand	127	1	20
α-helix	128-130	3
β-strand	132	1	20
β-strand	135-147	13	19
α-helix	149-151	3
β-strand	154-172	19	19
β-strand	178-184	7	19
α-helix	193-196	4
α-helix	200-205	6
α-helix	209-212	4
α-helix	223-231	9
α-helix	233-237	5
α-helix	242-245	4
α-helix	246-248	3
α-helix	250-262	13
α-helix	270-272	3
α-helix	277-287	11
α-helix	292-300	9
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	413-418	6	22
α-helix	419-421	3
β-strand	422-424	3	21

Chain C: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	410-411	2	1
β-strand	418-419	2	1
α-helix	422-430	9
α-helix	433-437	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sal-like protein 4	C	protein	102	Homo sapiens	Q9UJQ4 (AlphaFold model)
DNA damage-binding protein 1	A	protein	860	Homo sapiens	Q16531 (AlphaFold model)
Protein cereblon	B	protein	485	Homo sapiens	Q96SW2 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>9NWT_1 Sal-like protein 4 (chains C)
MDWSHPQFEKSAVGLNDIFEAQKIEWHEGGGGSGENLYFQGGGRGTDSSLQIHLRSHTGE
RPFVCSVCAHRFTTKGNLKVHFHRHPQVKANPQLFAEFQDKV

Sequence of entity 2 (A), FASTA

>9NWT_2 DNA damage-binding protein 1 (chains A)
MGSSHHHHHHSAVDENLYFQGGGRMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKN
TRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGE
SIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFN
IRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEA
SMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDM
EGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKL
NVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGG
NGNSGEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQA
LSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCK
LGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKL
LASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEG
NFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHL
GEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNK
VIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGM
KREATADDLIKVVEELTRIH

Sequence of entity 3 (B), FASTA

>9NWT_3 Protein cereblon (chains B)
MDYKDDDDKSAVDENLYFQGGGRGGSAHIVMVDAYKPTKGGSGMAGEGDQQDAAHNMGNH
LPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDS
CQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGT
TAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAV
QLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRI
KKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNK
CTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTE
HSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDK
VILCL

Ligands and cofactors

ID	Name	Formula	Copies
QFC	Mezigdomide	C32 H30 F N5 O4	1
ZN	Zinc ion	Zn	2

Primary citation

Expanding the druggable zinc-finger proteome defines properties of drug-induced degradation. Slabicki, M., Park, J., Nowak, R.P. et al. Mol Cell (2025) 85:3184-3201.e14. DOI 10.1016/j.molcel.2025.07.019 · PubMed

Other PDB entries of the same protein (UniProt Q9UJQ4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7BQV 1.8 Å, Cereblon in complex with SALL4 and (S)-5-hydroxythalidomide
7BQU 1.9 Å, Cereblon in complex with SALL4 and (S)-thalidomide
8CUC 2.09 Å, Crystal structure analysis of SALL4 zinc finger domain in complex with DNA
7Y3I 2.45 Å, Structure of DNA bound SALL4
7Y3K 2.5 Å, Structure of SALL4 ZFC4 bound with 16 bp AT-rich dsDNA
5XWR 2.69 Å, Crystal Structure of RBBP4-peptide complex
9NWS 2.7 Å, Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449)
7Y3M 2.72 Å, Structure of SALL4 ZFC1 bound with 16 bp AT-rich dsDNA
8U16 2.9 Å, The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to Pomalidomide
8U15 2.95 Å, The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to CC-220
8U17 3.1 Å, The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-long bound to Pomalidomide
9SQ4 3.49 Å, Cryo-EM structure of the DDB1deltaB-CRBN-Pomalidomide complex bound to…

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