12BP: Human DDB1-CRBN-GSPT1

Cryo-EM structure of human DDB1-CRBN-GSPT1 in complex with GT19630. Determined by electron microscopy at 2.9 Å resolution. Released 26 Aug 2026.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 3
Atoms: 9,845
Mol. weight: 164.83 kDa
Ligands: A1DBR, ZN
Released: 26 Aug 2026

Explore 12BP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

12BP contains 23 α-helices and 106 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 X: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	530-537	8	1
β-strand	549-552	4	1
β-strand	554	1	2
β-strand	557	1	2
β-strand	560-565	6	1
β-strand	570	1	3
α-helix	576	1
β-strand	577	1	3
α-helix	578	1
β-strand	589-591	3	1
β-strand	594-597	4	1
β-strand	617-618	2	1
β-strand	623-625	3	1
β-strand	628-633	6	1

Chain Y: 11 helices, 67 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	13
β-strand	17-21	5	14
β-strand	30-35	6	14
β-strand	38-44	7	14
β-strand	49-56	8	14
β-strand	61-67	7	15
β-strand	76-81	6	15
β-strand	85-92	8	15
β-strand	99-107	9	15
β-strand	115	1	16
β-strand	121-124	4	17
β-strand	130-134	5	17
β-strand	136	1	16
β-strand	139-144	6	17
β-strand	155-158	4	17
β-strand	163-169	7	18
α-helix	170	1
β-strand	177-184	8	18
β-strand	187-194	8	18
β-strand	195-196	2	19
β-strand	201-202	2	19
β-strand	208	1	18
β-strand	212	1	18
β-strand	219-221	3	20
β-strand	229-232	4	20
β-strand	237-241	5	20
β-strand	244-248	5	20
β-strand	258-263	6	21
β-strand	270-275	6	21
β-strand	279-288	10	21
β-strand	296-307	12	21
β-strand	311-318	8	22
β-strand	321-326	6	22
β-strand	331-336	6	22
β-strand	347-353	7	22
β-strand	359-365	7	23
β-strand	374-379	6	23
α-helix	382-384	3
β-strand	386-391	6	23
β-strand	711-716	6	23
β-strand	720-727	8	24
β-strand	732-742	11	24
β-strand	750-751	2	24
β-strand	763-765	3	24
β-strand	785-795	11	24
β-strand	801-806	6	24
β-strand	811-819	9	25
β-strand	828-835	8	25
β-strand	845-854	10	25
β-strand	857-864	8	25
β-strand	870-876	7	26
β-strand	879-884	6	26
β-strand	887-893	7	26
β-strand	899-906	8	26
β-strand	913-917	5	27
β-strand	920-924	5	27
β-strand	929-935	7	27
β-strand	942-949	8	27
β-strand	956-959	4	28
β-strand	964-969	6	28
β-strand	973-979	7	28
α-helix	986-989	4
β-strand	992-999	8	28
β-strand	1004-1009	6	13
β-strand	1024-1032	9	13
β-strand	1037-1043	7	13
α-helix	1045-1059	15
α-helix	1063-1064	2
α-helix	1070-1074	5
β-strand	1076-1077	2	29
β-strand	1082-1083	2	29
β-strand	1086	1	28
β-strand	1088-1090	3	13
α-helix	1091-1095	5
α-helix	1096-1098	3
α-helix	1102-1109	8
α-helix	1127-1136	10
α-helix	1137-1139	3

Chain Z: 10 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	78	1	4
β-strand	82-83	2	4
β-strand	96-98	3	4
β-strand	101	1	5
α-helix	104-115	12
β-strand	119-124	6	4
β-strand	127	1	6
α-helix	128-130	3
β-strand	132	1	6
β-strand	135-143	9	4
β-strand	155	1	5
β-strand	158-172	15	4
β-strand	178-184	7	4
α-helix	204-206	3
α-helix	221-231	11
α-helix	232-235	4
α-helix	250-264	15
α-helix	277-287	11
α-helix	292-300	9
α-helix	304-315	12
β-strand	320-322	3	7
β-strand	332-333	2	7
α-helix	334-336	3
β-strand	337-338	2	8
β-strand	341	1	9
β-strand	344	1	9
β-strand	348-351	4	10
β-strand	355-358	4	10
β-strand	361-362	2	8
β-strand	371-375	5	11
β-strand	384-385	2	12
β-strand	386-390	5	11
β-strand	397-400	4	11
β-strand	402-404	3	12
β-strand	413-414	2	12
β-strand	417	1	11
β-strand	423-425	3	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic peptide chain release factor GTP-binding subunit ERF3A	X	protein	218	Homo sapiens	P15170 (AlphaFold model)
Protein cereblon	Z	protein	406	Homo sapiens	Q96SW2 (AlphaFold model)
DNA damage-binding protein 1	Y	protein	836	Homo sapiens	Q16531 (AlphaFold model)

Sequence of entity 1 (X), FASTA

>12BP_1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A (chains X)
MGSSHHHHHHSSGLVPRGSHMGPIRLPIVDKYKDMGTVVLGKLESGSICKGQQLVMMPNK
HNVEVLGILSDDVETDTVAPGENLKIRLKGIEEEEILPGFILCDPNNLCHSGRTFDAQIV
IIEHKSIICPGYNAVLHIHTCIEEVEITALICLVDKKSGEKSKTRPRFVKQDQVCIARLR
TAGTICLETFKDFPQMGRFTLRDEGKTIAIGKVLKLVP

Sequence of entity 2 (Z), FASTA

>12BP_2 Protein cereblon (chains Z)
SNMEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQT
LPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVK
VKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSRE
DQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSN
PIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNE
IFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICAS
HIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL

Sequence of entity 3 (Y), FASTA

>12BP_3 DNA damage-binding protein 1 (chains Y)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGGNGNSGEIQKLHIRTVPLYESPRKI
CYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGE
EVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPK
QGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECN
HYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDN
FLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPT
QGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEP
ATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Ligands and cofactors

ID	Name	Formula	Copies
A1DBR	2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-N-[(4-{[2-(9H-pyrido[2,3-b]indol-9-yl)ac…	C35 H30 N6 O5	1
ZN	Zinc ion	Zn	1

Primary citation

Dual MYC and GSPT1 Protein Degrader for MYC-Driven Hematologic Malignancies. Nishida, Y., Impedovo, V., Ayoub, E. et al. Blood (2026). DOI 10.1182/blood.2025030170 · PubMed

Other PDB entries of the same protein (UniProt P15170 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3KUI 2.3 Å, Crystal structure of C-terminal domain of PABPC1 in complex with binding region of eRF3a
5HXB 3.6 Å, Cereblon in complex with DDB1, CC-885, and GSPT1
6XK9 3.64 Å, Cereblon in complex with DDB1, CC-90009, and GSPT1
5LZT 3.65 Å, Structure of the mammalian ribosomal termination complex with eRF1 and eRF3.
3E1Y 3.8 Å, Crystal structure of human eRF1/eRF3 complex
9HNE 3.9 Å, Cereblon in complex with DDB1, GSPT1 and Compound-1
4D61 9.0 Å, Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket…
3J5Y 9.7 Å, Structure of the mammalian ribosomal pre-termination complex associated with…

Browse structure collections

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