8OV6: DDB1deltaBPB

Ternary structure of intramolecular bivalent glue degrader IBG1 bound to BRD4 and DCAF16:DDB1deltaBPB. Determined by electron microscopy at 3.77 Å resolution. Released 17 May 2023.

Method: Electron microscopy
Resolution: 3.77 Å
Organism: Homo sapiens
Chains: 3
Atoms: 9,289
Mol. weight: 165.77 kDa
Ligands: U79, ZN
Released: 17 May 2023

Explore 8OV6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8OV6 contains 37 α-helices and 70 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: 11 helices, 68 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	1
β-strand	18-21	4	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	121-124	4	4
β-strand	130-136	7	4
β-strand	139-144	6	4
β-strand	155-158	4	4
β-strand	164-169	6	5
β-strand	177-184	8	5
β-strand	187-196	10	5
β-strand	201-204	4	5
β-strand	210-211	2	5
β-strand	218-221	4	6
β-strand	229-232	4	6
β-strand	237-241	5	6
β-strand	244-248	5	6
α-helix	251-255	5
β-strand	258-263	6	7
β-strand	270-275	6	7
β-strand	279-289	11	7
β-strand	295-307	13	7
β-strand	313-318	6	8
β-strand	321-325	5	8
β-strand	332-336	5	8
β-strand	347-352	6	8
β-strand	361-365	5	9
β-strand	374-379	6	9
α-helix	382-384	3
β-strand	386-392	7	9
β-strand	710-712	3	9
β-strand	716	1	9
β-strand	720-727	8	10
β-strand	732-742	11	10
β-strand	750-751	2	10
α-helix	756-758	3
β-strand	762-765	4	10
β-strand	785-795	11	10
β-strand	801-806	6	10
α-helix	807-808	2
β-strand	812-819	8	11
β-strand	828-834	7	11
β-strand	846-854	9	11
β-strand	857-866	10	11
β-strand	870-876	7	12
β-strand	879-884	6	12
β-strand	887-893	7	12
β-strand	899-903	5	12
β-strand	911-913	3	13
β-strand	916-917	2	13
β-strand	920-925	6	13
β-strand	928	1	14
β-strand	930-936	7	13
β-strand	941-947	7	13
β-strand	952	1	14
β-strand	954-959	6	15
β-strand	964-969	6	15
β-strand	973-979	7	15
α-helix	987-989	3
β-strand	991	1	13
β-strand	992-998	7	15
β-strand	1004-1008	5	1
β-strand	1025-1032	8	1
β-strand	1037-1042	6	1
α-helix	1045-1058	14
α-helix	1070-1073	4
β-strand	1076-1077	2	16
β-strand	1082-1083	2	16
β-strand	1086	1	15
β-strand	1088-1090	3	1
α-helix	1091-1095	5
α-helix	1096-1098	3
α-helix	1102-1109	8
α-helix	1126-1137	12

Chain B: 10 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	48-61	14
β-strand	66-67	2	17
α-helix	68-70	3
α-helix	74-76	3
α-helix	88-95	8
β-strand	99-100	2	17
α-helix	107-111	5
α-helix	116-119	4
α-helix	131-138	8
α-helix	143-156	14
α-helix	179-190	12
α-helix	201-215	15

Chain C: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	61-65	5
α-helix	66-70	5
α-helix	71-76	6
α-helix	81-83	3
α-helix	89-92	4
α-helix	97-100	4
α-helix	107-115	9
α-helix	123-139	17
α-helix	145-161	17
α-helix	350-364	15
α-helix	374-376	3
α-helix	379-381	3
α-helix	390-393	4
α-helix	400-408	9
α-helix	415-432	18
α-helix	438-454	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DDB1deltaBPB	A	protein	836	Homo sapiens	Q16531 (AlphaFold model)
DDB1- and CUL4-associated factor 16	B	protein	218	Homo sapiens	Q9NXF7 (AlphaFold model)
Bromodomain-containing protein 4	C	protein	419	Homo sapiens	O60885 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8OV6_1 DDB1deltaBPB (chains A)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGGNGNSGEIQKLHIRTVPLYESPRKI
CYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGE
EVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPK
QGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECN
HYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDN
FLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPT
QGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEP
ATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 2 (B), FASTA

>8OV6_2 DDB1- and CUL4-associated factor 16 (chains B)
GGMGPRNPSPDHLSESESEEEENISYLNESSGEEWDSSEEEDSMVPNLSPLESLAWQVKC
LLKYSTTWKPLNPNSWLYHAKLLDPSTPVHILREIGLRLSHCSHCVPKLEPIPEWPPLAS
CGVPPFQKPLTSPSRLSRDHATLNGALQFATKQLSRTLSRATPIPEYLKQIPNSCVSGCC
CGWLTKTVKETTRTEPINTTYSYTDFQKAVNKLLTASL

Sequence of entity 3 (C), FASTA

>8OV6_3 Bromodomain-containing protein 4 (chains C)
GSTNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKI
IKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQK
INELPTEETEIMIVQAKGRGRGRKETGTAKPGVSTVPNTTQASTPPQTQTPQPNPPPVQA
TPHPFPAVTPDLIVQTPVMTVVPPQPLQTPPPVPPQPQPPPAPAPQPVQSHPPIIAATPQ
PVKTKKGVKRKADTTTPTTIDPIHEPPSLPPEPKTTKLGQRRESSRPVKPPKKDVPDSQQ
HPAPEKSSKVSEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDM
STIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPD

Ligands and cofactors

ID	Name	Formula	Copies
U79	methyl 2-[(9~{S})-7-[4-[4-[[4-[(3-cyano-4-methyl-1~{H}-indol-7-yl)sulfamoyl]phe…	C44 H38 N8 O5 S2	1
ZN	Zinc ion	Zn	1

Primary citation

Targeted protein degradation via intramolecular bivalent glues. Hsia, O., Hinterndorfer, M., Cowan, A.D. et al. Nature (2024) 627:204-211. DOI 10.1038/s41586-024-07089-6 · 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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