9DHD: The ternary complex of DDB1, DDA1, DET1

The ternary complex of DDB1, DDA1, DET1. Determined by electron microscopy at 2.9 Å resolution. Released 5 Feb 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 3
Atoms: 10,063
Mol. weight: 205.66 kDa
Released: 5 Feb 2025

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

Secondary structure: helices and β-sheets

9DHD contains 30 α-helices and 96 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: 15 helices, 69 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	38-45	8	2
β-strand	48-56	9	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	151-154	4	3
β-strand	155-158	4	5
β-strand	164-169	6	6
α-helix	170	1
β-strand	177-184	8	6
β-strand	187-196	10	6
β-strand	201-204	4	6
β-strand	210-211	2	6
β-strand	218-221	4	7
α-helix	222-223	2
β-strand	229-232	4	7
β-strand	237-241	5	7
β-strand	244-248	5	7
α-helix	251-255	5
β-strand	258-263	6	8
β-strand	270-275	6	8
β-strand	279-289	11	8
β-strand	295-307	13	8
β-strand	311-318	8	9
β-strand	321-326	6	9
β-strand	331-336	6	9
β-strand	347-353	7	9
β-strand	361-365	5	10
β-strand	374-379	6	10
α-helix	382-384	3
β-strand	386-393	8	10
β-strand	709-716	8	10
β-strand	720-727	8	11
β-strand	732-742	11	11
β-strand	750-751	2	11
β-strand	762-765	4	11
β-strand	785-795	11	11
β-strand	801-806	6	11
β-strand	811-820	10	12
β-strand	827-835	9	12
β-strand	846-854	9	12
β-strand	857-866	10	12
β-strand	870-876	7	13
β-strand	879-884	6	13
β-strand	887-893	7	13
β-strand	899-905	7	13
β-strand	911-917	7	14
β-strand	920-925	6	14
β-strand	930-936	7	14
β-strand	941-947	7	14
β-strand	954-959	6	15
β-strand	964-969	6	15
β-strand	973-979	7	15
α-helix	988-990	3
β-strand	991	1	14
β-strand	992-999	8	15
β-strand	1004-1009	6	1
α-helix	1017-1021	5
β-strand	1024-1032	9	1
β-strand	1037-1043	7	1
α-helix	1045-1061	17
α-helix	1063-1064	2
α-helix	1070-1074	5
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	1091-1096	6
α-helix	1097-1099	3
α-helix	1102-1109	8
β-strand	1113-1115	3	17
β-strand	1121-1123	3	17
α-helix	1126-1136	11

Chain B: 12 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	18-27	10
α-helix	37-40	4
α-helix	41-44	4
β-strand	50-52	3	18
β-strand	60-65	6	19
β-strand	71-76	6	19
β-strand	81-87	7	19
α-helix	94-97	4
β-strand	104-105	2	18
α-helix	111-124	14
β-strand	125-132	8	19
β-strand	140	1	20
β-strand	146-147	2	20
β-strand	153-158	6	20
β-strand	189-197	9	20
β-strand	203-212	10	20
α-helix	217-219	3
β-strand	222-225	4	21
β-strand	228-233	6	21
β-strand	238-244	7	21
α-helix	245	1
β-strand	250-255	6	21
β-strand	331-338	8	22
β-strand	341-346	6	22
β-strand	364-369	6	22
β-strand	374-380	7	22
α-helix	384-398	15
α-helix	416-424	9
α-helix	449-451	3
α-helix	459-461	3
β-strand	466-468	3	23
α-helix	486	1
β-strand	487-491	5	23
β-strand	497-501	5	23
β-strand	517-522	6	18
β-strand	528-534	7	18
β-strand	539-545	7	18

Chain C: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	33	1
β-strand	34	1	2
α-helix	35	1
β-strand	45-49	5	3
α-helix	54-63	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A	protein	1155	Homo sapiens	Q16531 (AlphaFold model)
DET1 homolog	B	protein	557	Homo sapiens	Q7L5Y6 (AlphaFold model)
DET1- and DDB1-associated protein 1	C	protein	102	Homo sapiens	Q9BW61 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9DHD_1 DNA damage-binding protein 1 (chains A)
MHHHHHHHHGENLYFQSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVT
AEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAH
GNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVI
DVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEP
FGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLL
EKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGS
YVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLP
GIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAH
QQLIQITSASVRLVSQEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQE
LRQISHTEMEHEVACLDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGE
IIPRSILMTTFESSHYLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLS
TTNVFACSDRPTVIYSSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTID
EIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSV
SSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDP
NTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASIN
STVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEI
ARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVN
VFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSV
GKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREAT
ADDLIKVVEELTRIH

Sequence of entity 2 (B), FASTA

>9DHD_2 DET1 homolog (chains B)
MDYKDDDDKGENLYFQGSRIQNQNVIHRLERRRISSGKAGTHWHQVRVFHQNVFPNFTVV
NVEKPPCFLRKFSPDGRYFIAFSSDQTSLEIYEYQGCQAAEDLLQGYEGEILSNGNDQRS
VNIRGRLFERFFVLLHITNVAANGEHLNRECSLFTDDCRCVIVGSAAYLPDEPHPPFFEV
YRNSESVTPNPRSPLEDYSLHIIDLHTGRLCDTRTFKCDKVVLSHNQGLYLYKNILAILS
VQQQTIHVFQVTPEGTFIDVRTIGRFCYEDDLLTVSAVFPEVQRDSQTGMANPFRDPFIN
SLKHRLLVYLWRRAEQDGSAMAKRRFFQYFDQLRQLRMWKMQLLDENHLFIKYTSEDVVT
LRVTDPSQASFFVVYNMVTTEVIAVFENTSDELLELFENFCDLFRNATLHSEVQFPCSAS
SNNFARQIQRRFKDTIINAKYGGHTEAVRRLLGQLPISAQSYSGSPYLDLSLFSYDDKWV
SVMERPKTCGDHPIRFYARDSGLLKFEIQAGLLGRPINHTVRRLVAFTFHPFEPFAISVQ
RTNAEYVVNFHMRHCCT

Sequence of entity 3 (C), FASTA

>9DHD_3 DET1- and DDB1-associated protein 1 (chains C)
MADFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLH
QQWDKKNAAKKRDQEQVELEGESSAPPRKVARTDSPDMHEDT

Primary citation

Impairment of DET1 causes neurological defects and lethality in mice and humans. Karayel, O., Soung, A., Gurung, H. et al. Proc Natl Acad Sci U S A (2025) 122:e2422631122-e2422631122. DOI 10.1073/pnas.2422631122 · 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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