9V0A: Protein cereblon

Cryo-EM structure of pomalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly. Determined by electron microscopy at 3.69 Å resolution. Released 10 Jun 2026.

Method: Electron microscopy
Resolution: 3.69 Å
Organism: Homo sapiens
Chains: 8
Atoms: 20,800
Mol. weight: 318.66 kDa
Ligands: ZN, Y70
Released: 10 Jun 2026

Explore 9V0A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9V0A contains 81 α-helices and 157 β-strands across 8 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: 39 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	43	1	23
α-helix	58-74	17
α-helix	83-94	12
α-helix	99-114	16
α-helix	115-122	8
α-helix	128-152	25
α-helix	154-156	3
α-helix	157-161	5
α-helix	162-163	2
α-helix	168-169	2
α-helix	170-178	9
α-helix	179-183	5
α-helix	186-204	19
α-helix	212-223	12
α-helix	227	1
α-helix	228-232	5
α-helix	233-251	19
α-helix	256-276	21
α-helix	280-282	3
α-helix	284-294	11
α-helix	299-302	4
α-helix	303-307	5
α-helix	308-313	6
α-helix	316-326	11
α-helix	332-353	22
α-helix	358-360	3
α-helix	361-378	18
α-helix	384-398	15
α-helix	404-416	13
α-helix	426-440	15
α-helix	446-463	18
α-helix	469-514	46
β-strand	527-528	2	40
α-helix	534-535	2
α-helix	545-561	17
β-strand	565-570	6	40
β-strand	575-578	4	41
β-strand	589-592	4	41
α-helix	593-602	10
α-helix	610-617	8
α-helix	621-633	13
β-strand	639-642	4	42
β-strand	653-656	4	42
α-helix	693-707	15
α-helix	712-720	9
α-helix	730-741	12
β-strand	747	1	43
β-strand	755	1	43

Chain B: 16 helices, 104 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	12
β-strand	20-21	2	13
β-strand	30-34	5	13
β-strand	38-44	7	13
β-strand	49-56	8	13
β-strand	63-65	3	14
β-strand	77-80	4	14
β-strand	87-94	8	14
β-strand	97-105	9	14
α-helix	114	1
β-strand	115	1	15
α-helix	116	1
β-strand	121-124	4	16
β-strand	130-134	5	16
β-strand	136	1	15
β-strand	139-144	6	16
β-strand	155-158	4	16
β-strand	163-169	7	17
β-strand	177-184	8	17
β-strand	187-196	10	17
β-strand	201-204	4	17
β-strand	210-212	3	17
β-strand	218-221	4	18
β-strand	229-232	4	18
β-strand	237-240	4	18
β-strand	245-248	4	18
α-helix	253-255	3
β-strand	258-263	6	19
β-strand	270-275	6	19
β-strand	279-287	9	19
β-strand	297-307	11	19
α-helix	310-311	2
β-strand	313-316	4	20
β-strand	321-325	5	20
β-strand	332-336	5	20
β-strand	347-352	6	20
β-strand	359-365	7	21
α-helix	367-369	3
β-strand	374-379	6	21
β-strand	386-391	6	21
β-strand	394	1	22
β-strand	396-403	8	23
β-strand	410-413	4	24
β-strand	422	1	25
β-strand	424-428	5	24
β-strand	433-439	7	24
β-strand	442-445	4	24
β-strand	457-463	7	26
β-strand	467-472	6	26
β-strand	476-480	5	26
β-strand	486-490	5	26
α-helix	496-498	3
β-strand	500-503	4	27
β-strand	507-512	6	27
β-strand	515-522	8	27
β-strand	525-533	9	27
β-strand	538-542	5	28
β-strand	557-560	4	28
β-strand	565	1	29
β-strand	566-569	4	28
β-strand	576-578	3	28
β-strand	581	1	29
α-helix	587	1
β-strand	588-596	9	30
β-strand	599-606	8	30
β-strand	610-615	6	30
β-strand	624-630	7	30
β-strand	637-643	7	31
β-strand	646-652	7	31
β-strand	657-661	5	31
β-strand	666-670	5	31
β-strand	671	1	22
β-strand	678-682	5	23
β-strand	684	1	25
β-strand	690-694	5	23
β-strand	698-704	7	23
β-strand	711-712	2	21
β-strand	715-716	2	21
β-strand	720-727	8	32
β-strand	732-741	10	32
β-strand	751	1	32
β-strand	763-765	3	32
α-helix	766-768	3
β-strand	786-795	10	32
β-strand	801-806	6	32
α-helix	807-808	2
β-strand	811-819	9	33
β-strand	828-835	8	33
β-strand	845-854	10	33
β-strand	857-867	11	33
β-strand	870	1	34
β-strand	876	1	35
β-strand	879	1	35
β-strand	881	1	36
β-strand	884	1	34
β-strand	890-893	4	36
β-strand	899-903	5	36
β-strand	915-917	3	37
β-strand	920-922	3	37
β-strand	931-936	6	37
β-strand	941-947	7	37
β-strand	954-961	8	38
β-strand	964-969	6	38
β-strand	973-978	6	38
α-helix	987-990	4
β-strand	991	1	37
β-strand	993-999	7	38
β-strand	1007-1009	3	12
β-strand	1028-1030	3	12
β-strand	1037-1042	6	12
α-helix	1045-1061	17
α-helix	1070-1073	4
β-strand	1076-1078	3	39
β-strand	1081-1083	3	39
β-strand	1086	1	38
β-strand	1088-1090	3	12
α-helix	1091-1094	4
α-helix	1095-1099	5
α-helix	1102-1107	6
α-helix	1126-1137	12

Chain C: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	54-56	3
β-strand	79-83	5	1
β-strand	96-99	4	1
α-helix	104-111	8
β-strand	119-123	5	1
β-strand	135-141	7	1
β-strand	157-172	16	1
β-strand	178-184	7	1
α-helix	185-186	2
α-helix	193-196	4
α-helix	209-211	3
α-helix	221-231	11
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-264	15
α-helix	277-285	9
α-helix	292-300	9
α-helix	304-316	13
β-strand	321-322	2	2
β-strand	349-350	2	3
β-strand	356-357	2	3
β-strand	360-362	3	4
β-strand	368-370	3	4
β-strand	375	1	4
β-strand	384-391	8	4
β-strand	397-404	8	4
β-strand	415-417	3	4
β-strand	423-424	2	2

Chain D: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	4-15	12
β-strand	21-25	5	5
β-strand	32-37	6	5
β-strand	38	1	6
β-strand	49	1	6
β-strand	52-55	4	5
β-strand	66-69	4	5
β-strand	78	1	7
β-strand	84	1	7
α-helix	87-90	4
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-141	11
α-helix	142-146	5

Chain I: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	147	1	8
β-strand	154	1	8
α-helix	158-167	10
α-helix	186-194	9

Chain N: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	9
β-strand	12-16	5	9
β-strand	22	1	10
α-helix	23-33	11
β-strand	41-45	5	9
β-strand	48-49	2	9
β-strand	55	1	10
β-strand	65-71	7	9

Chain R: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	27	1	41
β-strand	30-35	6	40
α-helix	52-53	2
α-helix	54-57	4
β-strand	71	1	44
β-strand	73	1	45
β-strand	79	1	44
α-helix	82-90	9
β-strand	103	1	45

Chain U: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	11
β-strand	12-16	5	11
α-helix	23-33	11
β-strand	41-44	4	11
β-strand	49	1	11
α-helix	57-59	3
β-strand	65-71	7	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein cereblon	C	protein	427	Homo sapiens	Q96SW2 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 D1	D	protein	146	Homo sapiens	P51668 (AlphaFold model)
Zinc finger protein Aiolos	I	protein	58	Homo sapiens	Q9UKT9 (AlphaFold model)
NEDD8	N	protein	76	Homo sapiens	Q15843 (AlphaFold model)
Ubiquitin	U	protein	76	Homo sapiens	P62979
DNA damage-binding protein 1	B	protein	1140	Homo sapiens	Q16531
Cullin-4A	A	protein	775	Homo sapiens	Q13619
E3 ubiquitin-protein ligase RBX1, N-terminally processed	R	protein	111	Homo sapiens	P62877

Sequence of entity 1 (C), FASTA

>9V0A_1 Protein cereblon (chains C)
GSSHHHHHHHHSSGLEVLFQGPGSSAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDD
DSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQF
GTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMS
AVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMD
RIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIM
NKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPS
TEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISP
DKVILCL

Sequence of entity 2 (D), FASTA

>9V0A_2 Ubiquitin-conjugating enzyme E2 D1 (chains D)
ALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPTDYP
FKPPKIAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPNPDDPLVP
DIAQIYKSDKEKYNRHAREWTQKYAM

Sequence of entity 3 (I), FASTA

>9V0A_3 Zinc finger protein Aiolos (chains I)
GPGERPFQCNQCGASFTQKGNLLRHICLHTGEKPFKCHLCNYATQRRDALTGHLRTHS

Sequence of entity 4 (N), FASTA

>9V0A_4 NEDD8 (chains N)
MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK
ILGGSVLHLVLALRGG

Sequence of entity 5 (U), FASTA

>9V0A_5 Ubiquitin (chains U)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 6 (B), FASTA

>9V0A_6 DNA damage-binding protein 1 (chains B)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 7 (A), FASTA

>9V0A_7 Cullin-4A (chains A)
GPGSGWSHPQFEKGSGSADEAPRKGSFSALVGRTNGLTKPAALAAAPAKPGGAGGSKKLV
IKNFRDRPRLPDNYTQDTWRKLHEAVRAVQSSTSIRYNLEELYQAVENLCSHKVSPMLYK
QLRQACEDHVQAQILPFREDSLDSVLFLKKINTCWQDHCRQMIMIRSIFLFLDRTYVLQN
STLPSIWDMGLELFRTHIISDKMVQSKTIDGILLLIERERSGEAVDRSLLRSLLGMLSDL
QVYKDSFELKFLEETNCLYAAEGQRLMQEREVPEYLNHVSKRLEEEGDRVITYLDHSTQK
PLIACVEKQLLGEHLTAILQKGLDHLLDENRVPDLAQMYQLFSRVRGGQQALLQHWSEYI
KTFGTAIVINPEKDKDMVQDLLDFKDKVDHVIEVCFQKNERFVNLMKESFETFINKRPNK
PAELIAKHVDSKLRAGNKEATDEELERTLDKIMILFRFIHGKDVFEAFYKKDLAKRLLVG
KSASVDAEKSMLSKLKHECGAAFTSKLEGMFKDMELSKDIMVHFKQHMQNQSDSGPIDLT
VNILTMGYWPTYTPMEVHLTPEMIKLQEVFKAFYLGKHSGRKLQWQTTLGHAVLKAEFKE
GKKEFQVSLFQTLVLLMFNEGDGFSFEEIKMATGIEDSELRRTLQSLACGKARVLIKSPK
GKEVEDGDKFIFNGEFKHKLFRIKINQIQMKETVEEQVSTTERVFQDRQYQIDAAIVRIM
KMRKTLGHNLLVSELYNQLKFPVKPGDLKKRIESLIDRDYMERDKDNPNQYHYVA

Sequence of entity 8 (R), FASTA

>9V0A_8 E3 ubiquitin-protein ligase RBX1, N-terminally processed (chains R)
GPGSAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQ
ANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6
Y70	S-Pomalidomide	C13 H11 N3 O4	1

Primary citation

Cryo-EM structure of pomalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly. Deng, Z.H., Ai, H.S., Liu, L. To be published.

Other PDB entries of the same protein (UniProt Q96SW2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4M91 1.1 Å, crystal structure of hN33/Tusc3-peptide 1
9CUO 1.6 Å, Crystal structure of CRBN with compound 3
9OHQ 1.6 Å, Structure of CRBN:IKZF2:Compound 15
9DOM 1.69 Å, PVTX-405: A Potent, Highly Selective, and Orally Efficacious Molecular Glue Degrader of…
7BQV 1.8 Å, Cereblon in complex with SALL4 and (S)-5-hydroxythalidomide
9O91 1.86 Å, Structure of IKZF2:CRBN:Compound 5 ternary structure
7BQU 1.9 Å, Cereblon in complex with SALL4 and (S)-thalidomide
9GAO 1.95 Å, Crystal structure of CRBNmidi in complex with 2-(4-(2,6-dioxopiperidin-3-yl)phenoxy)-N-me…
9FJX 2.0 Å, Crystal structure of human CRBN-DDB1 in complex with Lenalidomide
8RQC 2.15 Å, Crystal structure of CRBN-midi in complex with mezigdomide and IKZF1 ZF2
8RQ8 2.19 Å, Crystal structure of CRBN-midi in complex with mezigdomide
9OHR 2.34 Å, Structure of CRBN:IKZF2:Compound 35

Browse structure collections

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