8D80: Cereblon~DDB1

Cereblon~DDB1 bound to Iberdomide and Ikaros ZF1-2-3. Determined by electron microscopy at 3.6 Å resolution. Released 20 Jul 2022.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 3
Atoms: 11,230
Mol. weight: 188.01 kDa
Ligands: ZN, 8W7
Released: 20 Jul 2022

Explore 8D80 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D80 contains 29 α-helices and 128 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: 14 helices, 106 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	1
β-strand	18-21	4	2
β-strand	30-34	5	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
α-helix	114	1
β-strand	115	1	4
α-helix	116	1
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
α-helix	170	1
β-strand	177-184	8	6
β-strand	187-194	8	6
β-strand	196	1	7
β-strand	201	1	7
β-strand	210-211	2	6
β-strand	218-221	4	8
β-strand	229-232	4	8
β-strand	237-240	4	8
β-strand	245-248	4	8
β-strand	258-263	6	9
β-strand	270-275	6	9
β-strand	279-284	6	9
β-strand	286	1	10
β-strand	289-290	2	11
β-strand	295-296	2	11
β-strand	299	1	10
β-strand	302-307	6	9
β-strand	311-313	3	12
β-strand	316	1	13
α-helix	318-320	3
β-strand	321-324	4	13
β-strand	325-326	2	12
β-strand	331-335	5	13
β-strand	348-353	6	13
α-helix	357	1
β-strand	359-365	7	14
β-strand	374-379	6	14
α-helix	382-384	3
β-strand	386-392	7	14
β-strand	394	1	15
β-strand	396-403	8	16
β-strand	409-413	5	17
β-strand	422	1	18
β-strand	424-428	5	17
β-strand	433-437	5	17
β-strand	444	1	17
β-strand	457-463	7	19
β-strand	467-472	6	19
β-strand	476-480	5	19
β-strand	489-490	2	19
β-strand	498-503	6	20
β-strand	507-512	6	20
β-strand	515-520	6	20
β-strand	527-533	7	20
β-strand	538-542	5	21
β-strand	556-560	5	21
β-strand	566-569	4	21
β-strand	576-580	5	21
α-helix	587	1
β-strand	588-595	8	22
β-strand	600-606	7	22
β-strand	611-612	2	22
β-strand	615	1	22
β-strand	616	1	23
β-strand	622	1	23
β-strand	628-629	2	22
β-strand	637-639	3	24
β-strand	649-652	4	24
β-strand	657-661	5	24
β-strand	666-668	3	24
β-strand	671	1	15
β-strand	678-682	5	16
β-strand	684	1	18
β-strand	690-694	5	16
β-strand	698-704	7	16
β-strand	710-716	7	14
β-strand	720-727	8	25
β-strand	732-743	12	25
β-strand	749-751	3	25
β-strand	764-765	2	25
β-strand	785-795	11	25
β-strand	801-806	6	25
β-strand	811-819	9	26
β-strand	828-835	8	26
β-strand	846-854	9	26
β-strand	857-866	10	26
β-strand	870-876	7	27
β-strand	879-884	6	27
β-strand	887-893	7	27
β-strand	899-906	8	27
β-strand	913-917	5	28
β-strand	920-924	5	28
β-strand	929-936	8	28
β-strand	941-949	9	28
β-strand	954-959	6	29
β-strand	964-969	6	29
β-strand	973-979	7	29
α-helix	986-989	4
β-strand	992-999	8	29
β-strand	1004-1009	6	1
β-strand	1025-1032	8	1
β-strand	1037-1042	6	1
α-helix	1045-1058	14
α-helix	1070-1074	5
β-strand	1076-1077	2	30
β-strand	1082-1083	2	30
β-strand	1088-1090	3	1
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1108	7
α-helix	1127-1137	11

Chain B: 14 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	53-56	4
β-strand	78-83	6	31
β-strand	96-101	6	32
α-helix	104-114	11
β-strand	119-125	7	32
β-strand	133-145	13	32
β-strand	155-166	12	32
β-strand	170	1	31
β-strand	178-183	6	31
β-strand	184-185	2	32
α-helix	186	1
β-strand	188	1	33
α-helix	201-203	3
α-helix	208-212	5
α-helix	223-231	9
α-helix	232-236	5
α-helix	242-247	6
α-helix	250-264	15
α-helix	277-287	11
α-helix	292-300	9
β-strand	303	1	33
α-helix	304-317	14
β-strand	321-322	2	34
α-helix	330-332	3
α-helix	334-336	3
β-strand	337	1	35
β-strand	346-350	5	36
β-strand	356-360	5	36
β-strand	361-362	2	35
β-strand	368-375	8	35
β-strand	385-391	7	35
β-strand	397-403	7	35
β-strand	415-416	2	35
β-strand	423-424	2	34

Chain C: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	146	1	37
β-strand	153	1	37
α-helix	158-167	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A	protein	1140	Homo sapiens	Q16531 (AlphaFold model)
Protein cereblon	B	protein	442	Homo sapiens	Q96SW2 (AlphaFold model)
DNA-binding protein Ikaros	C	protein	87	Homo sapiens	Q13422 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8D80_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

Sequence of entity 2 (B), FASTA

>8D80_2 Protein cereblon (chains B)
MAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYL
GADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTF
AVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQA
KVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSW
PRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLK
IGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETL
TVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRS
ALLPTIPDTEDEISPDKVILCL

Sequence of entity 3 (C), FASTA

>8D80_3 DNA-binding protein Ikaros (chains C)
GSLPNGKLKCDICGIICIGPNVLMVHKRSHTGERPFQCNQCGASFTQKGNLLRHIKLHSG
EKPFKCHLCNYACRRRDALTGHLRTHS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
8W7	(3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoi…	C25 H27 N3 O5	1

Primary citation

Molecular glue CELMoD compounds are regulators of cereblon conformation. Watson, E.R., Novick, S., Matyskiela, M.E. et al. Science (2022) 378:549-553. DOI 10.1126/science.add7574 · 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

Browse structure collections

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