9OS2: DDB1/CRBN-MRT-5702-G3BP2 ternary complex

Cryo-EM structure of the DDB1/CRBN-MRT-5702-G3BP2 ternary complex. Determined by electron microscopy at 2.5 Å resolution. Released 28 Jan 2026.

Method: Electron microscopy
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,132
Mol. weight: 279.73 kDa
Ligands: A1CED, ZN
Released: 28 Jan 2026

Explore 9OS2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9OS2 contains 41 α-helices and 103 β-strands across 4 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: 11 helices, 68 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	7
β-strand	17-21	5	8
β-strand	30-35	6	8
β-strand	38-44	7	8
β-strand	49-56	8	8
β-strand	61-67	7	9
β-strand	76-81	6	9
β-strand	85-92	8	9
β-strand	99-107	9	9
α-helix	114	1
β-strand	115	1	10
α-helix	116	1
β-strand	121-124	4	11
β-strand	130-134	5	11
β-strand	136	1	10
β-strand	139-144	6	11
β-strand	155-158	4	11
β-strand	163-169	7	12
α-helix	170	1
β-strand	177-184	8	12
β-strand	187-196	10	12
β-strand	201-204	4	12
β-strand	210-211	2	12
β-strand	218-221	4	13
β-strand	229-232	4	13
β-strand	237-241	5	13
β-strand	244-248	5	13
α-helix	251-255	5
β-strand	258-263	6	14
β-strand	270-275	6	14
β-strand	279-289	11	14
β-strand	295-307	13	14
β-strand	311-318	8	15
β-strand	321-326	6	15
β-strand	331-336	6	15
β-strand	347-353	7	15
β-strand	361-365	5	16
β-strand	372	1	17
β-strand	374-379	6	16
α-helix	382-384	3
β-strand	386-392	7	16
β-strand	710-716	7	16
β-strand	720-727	8	18
β-strand	732-742	11	18
β-strand	750-751	2	18
β-strand	762-765	4	18
β-strand	785-795	11	18
β-strand	801-806	6	18
β-strand	811-819	9	19
β-strand	828-835	8	19
β-strand	846-854	9	19
β-strand	857-866	10	19
β-strand	870-876	7	20
β-strand	879-884	6	20
β-strand	887-893	7	20
β-strand	899-906	8	20
β-strand	913-917	5	21
β-strand	920-924	5	21
β-strand	929-936	8	21
β-strand	941-949	9	21
β-strand	954-959	6	22
β-strand	964-969	6	22
β-strand	973-979	7	22
β-strand	991	1	21
β-strand	992-999	8	22
β-strand	1004-1009	6	7
β-strand	1014	1	17
β-strand	1025-1032	8	7
β-strand	1037-1042	6	7
α-helix	1045-1061	17
α-helix	1070-1074	5
β-strand	1076-1077	2	23
β-strand	1082-1083	2	23
β-strand	1086	1	22
β-strand	1088-1090	3	7
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1108	7
α-helix	1126-1137	12

Chain B: 18 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	52-56	5
α-helix	58-60	3
β-strand	65-66	2	1
α-helix	72-74	3
β-strand	78-81	4	1
β-strand	83	1	1
β-strand	96-101	6	1
α-helix	104-115	12
β-strand	119-125	7	1
β-strand	133-147	15	1
α-helix	149-151	3
β-strand	154-171	18	1
β-strand	179-184	6	1
α-helix	185-186	2
β-strand	188	1	2
α-helix	190-192	3
α-helix	195-197	3
α-helix	200-205	6
α-helix	220-231	12
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	320-321	2	3
β-strand	322-323	2	4
β-strand	332-333	2	3
α-helix	334-336	3
β-strand	337	1	5
β-strand	341	1	6
β-strand	344	1	6
β-strand	346-350	5	5
β-strand	356-362	7	5
β-strand	368-375	8	5
β-strand	384-391	8	5
β-strand	397-404	8	5
β-strand	413-418	6	5
α-helix	419-421	3
β-strand	422-423	2	4

Chain C: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
α-helix	27-33	7
β-strand	34-41	8	24
β-strand	55-56	2	24
α-helix	58-66	9
β-strand	74-85	12	24
α-helix	86-88	3
β-strand	89-99	11	24
α-helix	103-105	3
β-strand	106-116	11	24
β-strand	124-133	10	24
α-helix	134-137	4

Chain D: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-25	17
α-helix	27-33	7
β-strand	34-41	8	25
β-strand	55-56	2	25
α-helix	58-68	11
β-strand	74-85	12	25
α-helix	86-88	3
β-strand	89-99	11	25
α-helix	103-105	3
β-strand	106-116	11	25
β-strand	124-133	10	25
α-helix	134-137	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein cereblon	B	protein	378	Homo sapiens	Q96SW2 (AlphaFold model)
DNA damage-binding protein 1	A	protein	1140	Homo sapiens	Q16531 (AlphaFold model)
Ras GTPase-activating protein-binding protein 2	C, D	protein	482	Homo sapiens	Q9UN86 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9OS2_1 Protein cereblon (chains B)
INFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQE
VSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFK
VLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQK
YQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAA
CLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPM
AAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATK
KDMSPQKFWGLTRSALLP

Sequence of entity 2 (A), FASTA

>9OS2_2 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 3 (C, D), FASTA

>9OS2_3 Ras GTPase-activating protein-binding protein 2 (chains C, D)
MVMEKPSPLLVGREFVRQYYTLLNKAPEYLHRFYGRNSSYVHGGVDASGKPQEAVYGQND
IHHKVLSLNFSECHTKIRHVDAHATLSDGVVVQVMGLLSNSGQPERKFMQTFVLAPEGSV
PNKFYVHNDMFRYEDEVFGDSEPELDEESEDEVEEEQEERQPSPEPVQENANSGYYEAHP
VTNGIEEPLEESSHEPEPEPESETKTEELKPQVEEKNLEELEEKSTTPPPAEPVSLPQEP
PKAFSWASVTSKNLPPSGTVSSSGIPPHVKAPVSQPRVEAKPEVQSQPPRVREQRPRERP
GFPPRGPRPGRGDMEQNDSDNRRIIRYPDSHQLFVGNLPHDIDENELKEFFMSFGNVVEL
RINTKGVGGKLPNFGFVVFDDSEPVQRILIAKPIMFRGEVRLNVEEKKTRAARERETRGG
GDDRRDIRRNDRGPGGPRGIVGGGMMRDRDGRGPPPRGGMAQKLGSGRGTGQMEGRFTGQ
RR

Ligands and cofactors

ID	Name	Formula	Copies
A1CED	(1S,3S)-2-[(2-chlorophenyl)methanesulfonyl]-N-{[(4R)-3-(2,4-dioxo-1,3-diazinan-…	C30 H29 Cl N6 O5 S	1
ZN	Zinc ion	Zn	1

Primary citation

Cereblon induces G3BP2 neosubstrate degradation using molecular surface mimicry. Annunziato, S., Quan, C., Donckele, E.J. et al. Nat Struct Mol Biol (2026) 33:479-487. DOI 10.1038/s41594-025-01738-8 · 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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