8U16: Protein cereblon

The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to Pomalidomide. Determined by X-ray diffraction at 2.9 Å resolution. Released 27 Dec 2023.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 6
Atoms: 18,095
Mol. weight: 286.47 kDa
Ligands: Y70, ZN
Released: 27 Dec 2023

Explore 8U16 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8U16 contains 66 α-helices and 179 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: 16 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	78-83	6	1
α-helix	91-92	2
β-strand	96-101	6	1
α-helix	104-113	10
β-strand	119-125	7	1
β-strand	133-147	15	1
α-helix	149-151	3
β-strand	154-172	19	1
α-helix	177	1
β-strand	178-184	7	1
α-helix	185-186	2
α-helix	200-205	6
α-helix	222-231	10
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-264	15
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	2
β-strand	330-333	4	2
α-helix	334-336	3
β-strand	337	1	3
β-strand	341	1	4
β-strand	344	1	4
β-strand	346-350	5	3
β-strand	356-362	7	3
β-strand	368-375	8	3
β-strand	384-391	8	3
β-strand	397-404	8	3
β-strand	413-418	6	3
α-helix	419-421	3
β-strand	422-425	4	2

Chain B: 15 helices, 68 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	5
β-strand	17-21	5	6
β-strand	30-35	6	6
β-strand	38-44	7	6
β-strand	49-56	8	6
β-strand	61-67	7	7
β-strand	76-81	6	7
β-strand	85-94	10	7
β-strand	97-107	11	7
α-helix	114	1
β-strand	115	1	8
α-helix	116	1
β-strand	121-124	4	9
β-strand	130-134	5	9
β-strand	136	1	8
β-strand	139-144	6	9
β-strand	155-158	4	9
β-strand	164-169	6	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	258-263	6	12
β-strand	270-275	6	12
β-strand	279-289	11	12
β-strand	295-307	13	12
β-strand	313-318	6	13
β-strand	321-325	5	13
β-strand	331-336	6	13
β-strand	347-353	7	13
β-strand	359-365	7	14
β-strand	374-379	6	14
α-helix	382-384	3
β-strand	386-391	6	14
β-strand	711-716	6	14
β-strand	720-727	8	15
α-helix	728-730	3
β-strand	732-743	12	15
β-strand	749-751	3	15
α-helix	756-758	3
β-strand	762-765	4	15
β-strand	785-795	11	15
β-strand	801-806	6	15
β-strand	811-820	10	16
β-strand	827-835	9	16
β-strand	846-851	6	16
β-strand	860-866	7	16
β-strand	873-876	4	17
β-strand	879-884	6	17
β-strand	887-893	7	17
β-strand	899-906	8	17
β-strand	913-917	5	18
β-strand	920-924	5	18
β-strand	930-936	7	18
β-strand	941-948	8	18
β-strand	954-961	8	19
β-strand	964-969	6	19
β-strand	973-979	7	19
α-helix	986-989	4
β-strand	991	1	18
β-strand	992-999	8	19
β-strand	1004-1009	6	5
β-strand	1025-1032	8	5
β-strand	1037-1043	7	5
α-helix	1045-1059	15
α-helix	1063-1064	2
α-helix	1070-1073	4
β-strand	1076-1077	2	20
β-strand	1082-1083	2	20
β-strand	1086	1	19
β-strand	1088-1090	3	5
α-helix	1091-1095	5
α-helix	1102-1109	8
β-strand	1113-1114	2	21
β-strand	1122-1123	2	21
α-helix	1124-1125	2
α-helix	1126-1137	12

Chains C and F: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	382-383	2	22
β-strand	390-391	2	22
α-helix	394-401	8
α-helix	402-404	3
β-strand	410-411	2	23
β-strand	418-419	2	23
α-helix	422-429	8

Chain D: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	78-83	6	24
α-helix	91-92	2
β-strand	96-101	6	24
α-helix	104-115	12
β-strand	119-125	7	24
β-strand	133-147	15	24
α-helix	149-151	3
β-strand	154-171	18	24
β-strand	179-184	6	24
α-helix	185-186	2
α-helix	200-205	6
α-helix	221-231	11
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-264	15
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	25
β-strand	330-333	4	25
α-helix	334-336	3
β-strand	337	1	26
β-strand	341	1	27
β-strand	344	1	27
β-strand	346-350	5	26
β-strand	356-362	7	26
β-strand	368-375	8	26
β-strand	384-391	8	26
β-strand	397-404	8	26
β-strand	413-418	6	26
α-helix	419-421	3
β-strand	422-425	4	25

Chain E: 14 helices, 67 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	28
β-strand	17-21	5	29
β-strand	30-35	6	29
β-strand	38-44	7	29
β-strand	49-56	8	29
β-strand	61-67	7	30
β-strand	76-81	6	30
β-strand	85-94	10	30
β-strand	97-107	11	30
α-helix	114	1
β-strand	115	1	31
α-helix	116	1
β-strand	121-124	4	32
β-strand	130-134	5	32
β-strand	136	1	31
β-strand	139-144	6	32
β-strand	155-158	4	32
β-strand	164-169	6	33
α-helix	170	1
β-strand	177-184	8	33
β-strand	187-196	10	33
β-strand	201-209	9	33
β-strand	218-221	4	34
β-strand	229-232	4	34
β-strand	237-241	5	34
β-strand	244-248	5	34
α-helix	251-253	3
β-strand	258-263	6	35
β-strand	270-275	6	35
β-strand	279-289	11	35
β-strand	295-307	13	35
β-strand	313-316	4	36
β-strand	321-325	5	36
β-strand	331-336	6	36
β-strand	347-353	7	36
β-strand	359-365	7	37
β-strand	374-379	6	37
α-helix	382-384	3
β-strand	386-391	6	37
β-strand	711-716	6	37
β-strand	720-727	8	38
α-helix	728-730	3
β-strand	732-742	11	38
β-strand	750-751	2	38
β-strand	762-765	4	38
β-strand	785-795	11	38
β-strand	801-806	6	38
β-strand	811-820	10	39
β-strand	827-835	9	39
β-strand	846-854	9	39
β-strand	857-866	10	39
β-strand	872-876	5	40
β-strand	879-884	6	40
β-strand	887-893	7	40
β-strand	899-906	8	40
β-strand	913-917	5	41
β-strand	920-924	5	41
β-strand	930-936	7	41
β-strand	941-948	8	41
β-strand	954-961	8	42
β-strand	964-969	6	42
β-strand	973-979	7	42
α-helix	986-989	4
β-strand	991	1	41
β-strand	992-999	8	42
β-strand	1004-1009	6	28
β-strand	1025-1032	8	28
β-strand	1037-1042	6	28
α-helix	1045-1059	15
α-helix	1063-1064	2
α-helix	1070-1073	4
β-strand	1076-1077	2	43
β-strand	1082-1083	2	43
β-strand	1086	1	42
β-strand	1088-1090	3	28
α-helix	1091-1095	5
α-helix	1102-1108	7
β-strand	1113-1114	2	44
β-strand	1122-1123	2	44
α-helix	1124-1125	2
α-helix	1126-1137	12

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	55	Homo sapiens	Q9UJQ4 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>8U16_1 Protein cereblon (chains A, D)
RTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQ
EREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECV
LPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYD
AETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLR
CELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLN
LIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDT
EDEISPDKVILCL

Sequence of entity 2 (B, E), FASTA

>8U16_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

>8U16_3 Sal-like protein 4 (chains C, F)
SLYKHKCKYCSKVFGTDSSLQIHLRSHTGERPFVCSVCGHRFTTKGNLKVHFHRH

Ligands and cofactors

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

Water and common crystallization additives (EDO) are not listed.

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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