8OIZ: Human CRBN-DDB1

Crystal structure of human CRBN-DDB1 in complex with Pomalidomide. Determined by X-ray diffraction at 2.5 Å resolution. Released 19 Jul 2023.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 11,765
Mol. weight: 175.6 kDa
Ligands: ZN, Y70
Released: 19 Jul 2023

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

Secondary structure: helices and β-sheets

8OIZ contains 34 α-helices and 122 β-strands across 2 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: 18 helices, 99 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
β-strand	177-184	8	6
β-strand	187-196	10	6
β-strand	201-209	9	6
β-strand	218-221	4	7
β-strand	229-232	4	7
β-strand	237-240	4	7
β-strand	245-248	4	7
α-helix	251-253	3
β-strand	258-263	6	8
β-strand	270-275	6	8
β-strand	279-286	8	8
β-strand	299-307	9	8
β-strand	313-316	4	9
β-strand	321-325	5	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	386-393	8	10
β-strand	394	1	11
β-strand	396-403	8	12
β-strand	409-413	5	13
β-strand	424-429	6	13
β-strand	432-439	8	13
β-strand	442-446	5	13
β-strand	457-463	7	14
β-strand	467-472	6	14
β-strand	476-480	5	14
β-strand	486-490	5	14
α-helix	496-498	3
β-strand	500-503	4	15
β-strand	507-512	6	15
β-strand	515-522	8	15
β-strand	525-533	9	15
β-strand	538-542	5	16
β-strand	555-560	6	16
β-strand	565-570	6	16
β-strand	576-581	6	16
α-helix	586-587	2
β-strand	588-596	9	17
β-strand	599-606	8	17
β-strand	610-615	6	17
β-strand	616	1	18
β-strand	623	1	18
β-strand	627-630	4	17
α-helix	635-636	2
β-strand	637-643	7	19
β-strand	646-652	7	19
β-strand	657-662	6	19
β-strand	665-670	6	19
β-strand	671	1	11
β-strand	678-682	5	12
β-strand	690-694	5	12
β-strand	698-704	7	12
β-strand	709-716	8	10
β-strand	720-727	8	20
α-helix	728-730	3
β-strand	732-742	11	20
β-strand	750-751	2	20
α-helix	756-758	3
β-strand	762-765	4	20
β-strand	785-795	11	20
β-strand	801-806	6	20
α-helix	807-808	2
β-strand	811-819	9	21
β-strand	828-835	8	21
β-strand	846-854	9	21
β-strand	857-866	10	21
β-strand	870-876	7	22
β-strand	879-884	6	22
β-strand	887-893	7	22
β-strand	899-906	8	22
β-strand	913-917	5	23
β-strand	920-924	5	23
β-strand	930-936	7	23
β-strand	941-948	8	23
β-strand	954-961	8	24
β-strand	964-969	6	24
β-strand	973-979	7	24
α-helix	986-989	4
β-strand	991	1	23
β-strand	992-999	8	24
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	1063-1064	2
α-helix	1070-1074	5
β-strand	1076-1077	2	25
β-strand	1082-1083	2	25
β-strand	1086	1	24
β-strand	1088-1090	3	1
α-helix	1091-1094	4
α-helix	1095-1099	5
α-helix	1102-1109	8
β-strand	1113-1114	2	26
β-strand	1122-1123	2	26
α-helix	1124	1
α-helix	1126-1137	12
α-helix	1141-1145	5

Chain B: 16 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	47	1	27
α-helix	54-56	3
α-helix	58-60	3
β-strand	65-66	2	28
α-helix	73-74	2
β-strand	78-83	6	28
β-strand	96-101	6	28
α-helix	104-114	11
β-strand	119-127	9	28
β-strand	132-147	16	28
α-helix	149-151	3
β-strand	154-172	19	28
β-strand	178-184	7	28
α-helix	185-187	3
β-strand	188	1	29
α-helix	203-205	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
β-strand	303	1	29
α-helix	304-317	14
β-strand	320-323	4	30
β-strand	330-333	4	30
α-helix	334-336	3
β-strand	337	1	31
β-strand	341	1	32
β-strand	344	1	32
β-strand	346-350	5	31
β-strand	356-362	7	31
β-strand	368-375	8	31
β-strand	384-391	8	31
β-strand	397-404	8	31
β-strand	410	1	27
β-strand	413-418	6	31
α-helix	419-421	3
β-strand	422-425	4	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A	protein	1148	Homo sapiens	Q16531 (AlphaFold model)
Protein cereblon	B	protein	407	Homo sapiens	Q96SW2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8OIZ_1 DNA damage-binding protein 1 (chains A)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH
WSHPQFEK

Sequence of entity 2 (B), FASTA

>8OIZ_2 Protein cereblon (chains B)
GPHMEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQ
TLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIV
KVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSR
EDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPS
NPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKN
EIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICA
SHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL

Ligands and cofactors

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

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

Primary citation

A Degron Blocking Strategy Towards Improved CRL4 CRBN Recruiting PROTAC Selectivity. Bouguenina, H., Scarpino, A., O'Hanlon, J.A. et al. Chembiochem (2023) 24:e202300351-e202300351. DOI 10.1002/cbic.202300351 · 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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