8U17: Protein cereblon

The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-long bound to Pomalidomide. Determined by X-ray diffraction at 3.1 Å resolution. Released 27 Dec 2023.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 6
Atoms: 17,033
Mol. weight: 292.95 kDa
Ligands: Y70, ZN
Released: 27 Dec 2023

Explore 8U17 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8U17 contains 53 α-helices and 196 β-strands across 6 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: 14 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	78-81	4	1
β-strand	83	1	1
α-helix	91-92	2
β-strand	93	1	1
β-strand	96-98	3	1
β-strand	101	1	1
α-helix	104-115	12
β-strand	119-123	5	1
β-strand	135-149	15	1
β-strand	152-169	18	1
β-strand	180-184	5	1
α-helix	185-187	3
β-strand	188	1	2
α-helix	203-206	4
α-helix	209-212	4
α-helix	223-232	10
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-264	15
α-helix	277-286	10
α-helix	292-300	9
β-strand	303	1	2
α-helix	304-317	14
β-strand	320-323	4	3
β-strand	330-333	4	3
α-helix	334-336	3
β-strand	341	1	4
β-strand	344	1	4
β-strand	346-350	5	5
β-strand	356-362	7	5
β-strand	375	1	5
β-strand	386-390	5	5
β-strand	397-402	6	5
β-strand	414-418	5	5
α-helix	419-421	3
β-strand	422-425	4	3

Chain B: 10 helices, 69 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	6
β-strand	17-21	5	7
β-strand	30-35	6	7
β-strand	38-44	7	7
β-strand	49-56	8	7
β-strand	61-67	7	8
β-strand	76-81	6	8
β-strand	85-94	10	8
β-strand	97-107	11	8
β-strand	115	1	9
β-strand	121-124	4	9
β-strand	130-136	7	9
β-strand	139-144	6	9
β-strand	155	1	9
β-strand	158	1	9
β-strand	163-169	7	10
α-helix	170	1
β-strand	177-184	8	10
β-strand	187-196	10	10
β-strand	201-203	3	10
β-strand	208-209	2	10
β-strand	218-221	4	11
β-strand	229-232	4	11
β-strand	237-241	5	11
β-strand	244-248	5	11
α-helix	251-253	3
β-strand	260-263	4	12
β-strand	270-274	5	12
β-strand	279-286	8	12
β-strand	289	1	13
β-strand	295	1	13
β-strand	299-307	9	12
β-strand	311-318	8	14
β-strand	321-326	6	14
β-strand	331-336	6	14
β-strand	347-353	7	14
β-strand	361-363	3	15
β-strand	375-379	5	15
α-helix	382-384	3
β-strand	386-390	5	15
β-strand	712	1	15
β-strand	715-716	2	15
β-strand	720-727	8	16
β-strand	732-743	12	16
β-strand	749-751	3	16
β-strand	762-765	4	16
β-strand	785-795	11	16
β-strand	801-806	6	16
β-strand	811-821	11	17
β-strand	824-835	12	17
β-strand	846-853	8	17
β-strand	858-866	9	17
β-strand	870-875	6	18
β-strand	879-884	6	18
β-strand	887-893	7	18
β-strand	899-905	7	18
β-strand	913-917	5	19
β-strand	920-924	5	19
β-strand	930-936	7	19
β-strand	941-948	8	19
β-strand	954-959	6	20
β-strand	965-969	5	20
β-strand	973-978	6	20
β-strand	991	1	19
α-helix	992	1
β-strand	993-999	7	20
β-strand	1004-1009	6	6
β-strand	1025-1032	8	6
β-strand	1037-1043	7	6
α-helix	1045-1058	14
α-helix	1063-1064	2
α-helix	1070-1074	5
β-strand	1076-1077	2	21
β-strand	1082-1083	2	21
β-strand	1086	1	20
β-strand	1090	1	6
α-helix	1091-1094	4
α-helix	1102-1108	7
α-helix	1127-1137	11

Chains C and F: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	383	1	22
β-strand	390	1	22
α-helix	394-401	8
β-strand	410-411	2	23
β-strand	418-419	2	23
α-helix	422-430	9

Chain D: 15 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	78-81	4	24
β-strand	83	1	24
α-helix	91-92	2
β-strand	96-98	3	24
β-strand	101	1	24
α-helix	104-115	12
β-strand	119-123	5	24
β-strand	135-149	15	24
β-strand	152-172	21	24
β-strand	178-184	7	24
α-helix	185-187	3
β-strand	188	1	25
α-helix	203-206	4
α-helix	209-211	3
α-helix	223-231	9
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-264	15
α-helix	270-272	3
α-helix	277-286	10
α-helix	292-300	9
β-strand	303	1	25
α-helix	304-317	14
β-strand	320-322	3	26
β-strand	330-333	4	26
α-helix	334-336	3
β-strand	341	1	27
β-strand	344	1	27
β-strand	346-350	5	28
β-strand	356-360	5	28
β-strand	371-375	5	28
β-strand	384-385	2	29
β-strand	386-390	5	28
β-strand	397-401	5	28
β-strand	403-404	2	29
β-strand	415-418	4	28
α-helix	419-421	3
β-strand	423-425	3	26

Chain E: 10 helices, 74 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	30
β-strand	17-21	5	31
β-strand	30-35	6	31
β-strand	38-44	7	31
β-strand	49-56	8	31
β-strand	61-67	7	32
β-strand	76-81	6	32
β-strand	85-94	10	32
β-strand	97-107	11	32
β-strand	115	1	33
β-strand	121-124	4	33
β-strand	130-136	7	33
β-strand	139-144	6	33
β-strand	155	1	33
β-strand	158	1	33
β-strand	164-169	6	34
α-helix	170	1
β-strand	171	1	35
β-strand	177-184	8	34
β-strand	187-195	9	34
β-strand	202-203	2	34
β-strand	208-209	2	34
β-strand	218-221	4	36
β-strand	228	1	35
β-strand	229-232	4	36
β-strand	237-241	5	36
β-strand	244-248	5	36
α-helix	251-253	3
β-strand	260-263	4	37
β-strand	270-274	5	37
β-strand	279-286	8	37
β-strand	289	1	38
β-strand	295	1	38
β-strand	299-307	9	37
β-strand	313-318	6	39
β-strand	321-325	5	39
β-strand	331-336	6	39
β-strand	347-353	7	39
β-strand	361-363	3	40
β-strand	375-379	5	40
α-helix	382-384	3
β-strand	386-390	5	40
β-strand	712-716	5	40
β-strand	720-727	8	41
β-strand	732-743	12	41
β-strand	749-751	3	41
β-strand	762-765	4	41
β-strand	785-795	11	41
β-strand	801-806	6	41
β-strand	813-819	7	42
β-strand	821	1	43
β-strand	828-833	6	42
β-strand	846-853	8	42
β-strand	858-866	9	42
β-strand	870-875	6	44
β-strand	878	1	43
β-strand	879-884	6	44
β-strand	887-893	7	44
β-strand	899-905	7	44
β-strand	913-917	5	45
β-strand	920-924	5	45
β-strand	930-934	5	45
β-strand	935-936	2	46
β-strand	941-942	2	46
β-strand	946-948	3	45
β-strand	956-959	4	47
β-strand	965-968	4	47
β-strand	973-978	6	47
β-strand	991	1	45
α-helix	992	1
β-strand	993-999	7	47
β-strand	1004-1009	6	30
β-strand	1025-1032	8	30
β-strand	1037-1043	7	30
α-helix	1045-1058	14
α-helix	1063-1064	2
α-helix	1070-1074	5
β-strand	1076-1077	2	48
β-strand	1082-1083	2	48
β-strand	1086	1	47
β-strand	1090	1	30
α-helix	1091-1094	4
α-helix	1102-1108	7
α-helix	1126-1138	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein cereblon	A, D	protein	373	Homo sapiens	Q96SW2 (AlphaFold model)
DNA damage-binding protein 1	B, E	protein	836	Homo sapiens	Q16531 (AlphaFold model)
Sal-like protein 4	C, F	protein	86	Homo sapiens	Q9UJQ4 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>8U17_1 Protein cereblon (chains A, D)
RTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQ
EREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECV
LPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYD
AETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLR
CELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLN
LIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDT
EDEISPDKVILCL

Sequence of entity 2 (B, E), FASTA

>8U17_2 DNA damage-binding protein 1 (chains B, E)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGGNGNSGEIQKLHIRTVPLYESPRKI
CYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGE
EVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPK
QGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECN
HYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDN
FLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPT
QGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEP
ATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 3 (C, F), FASTA

>8U17_3 Sal-like protein 4 (chains C, F)
SDVKPKDEAALYKHKCKYCSKVFGTDSSLQIHLRSHTGERPFVCSVCGHRFTTKGNLKVH
FHRHPQVKANPQLFAEFQDKVAAGNG

Ligands and cofactors

ID	Name	Formula	Copies
Y70	S-Pomalidomide	C13 H11 N3 O4	2
ZN	Zinc ion	Zn	6

Primary citation

Structural and biophysical comparisons of the pomalidomide- and CC-220-induced interactions of SALL4 with cereblon. Ma, X., Leon, B., Ornelas, E. et al. Sci Rep (2023) 13:22088-22088. DOI 10.1038/s41598-023-48606-3 · PubMed

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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