9LTJ: DDB1-DDA1-DET1 complex

Name: PDB 9LTJ: Cryo-EM structure of DDB1-DDA1-DET1 complex
Published: 2026-01-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Cryo-EM structure of DDB1-DDA1-DET1 complex. Determined by electron microscopy at 2.65 Å resolution. Released 28 Jan 2026.

Method: Electron microscopy
Resolution: 2.65 Å
Organism: Homo sapiens
Chains: 3
Atoms: 8,861
Mol. weight: 202.88 kDa
Released: 28 Jan 2026

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

Secondary structure: helices and β-sheets

9LTJ contains 26 α-helices and 102 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: 12 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	18-27	10
α-helix	35-40	6
β-strand	51	1	1
β-strand	52-53	2	2
β-strand	61-65	5	3
β-strand	71-75	5	3
β-strand	81	1	4
β-strand	83-87	5	3
α-helix	95-97	3
β-strand	104	1	1
α-helix	121-123	3
β-strand	125-129	5	3
β-strand	132	1	4
β-strand	139-140	2	5
β-strand	147	1	5
β-strand	154-159	6	5
β-strand	192-196	5	5
β-strand	203-207	5	5
β-strand	222-224	3	6
β-strand	229-231	3	6
β-strand	240-244	5	6
β-strand	250-255	6	6
β-strand	333	1	7
β-strand	341-342	2	8
β-strand	345	1	7
β-strand	367-369	3	8
β-strand	374-377	4	8
α-helix	384-392	9
α-helix	394-396	3
α-helix	419-430	12
α-helix	437-440	4
α-helix	448	1
α-helix	450-451	2
α-helix	459-461	3
β-strand	466-467	2	9
β-strand	488-491	4	9
β-strand	497-500	4	9
β-strand	519-522	4	2
α-helix	523	1
β-strand	528-534	7	2
β-strand	539-545	7	2

Chain B: 12 helices, 71 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	10
β-strand	17-21	5	11
β-strand	30-35	6	11
β-strand	38-45	8	11
β-strand	48-56	9	11
β-strand	61-67	7	12
β-strand	76-81	6	12
β-strand	85-94	10	12
β-strand	97-107	11	12
α-helix	114	1
β-strand	115	1	13
α-helix	116	1
β-strand	121-124	4	14
β-strand	130-134	5	14
β-strand	136	1	13
β-strand	139-144	6	14
β-strand	151-154	4	15
β-strand	155-158	4	14
β-strand	164-169	6	16
α-helix	170	1
β-strand	177-184	8	16
β-strand	187-196	10	16
β-strand	201-204	4	16
β-strand	210-212	3	16
β-strand	218-221	4	17
β-strand	229-232	4	17
β-strand	237-241	5	17
β-strand	244-248	5	17
α-helix	253-255	3
β-strand	258-263	6	18
β-strand	270-275	6	18
β-strand	279-289	11	18
β-strand	295-307	13	18
β-strand	313-318	6	19
β-strand	321-325	5	19
β-strand	331-336	6	19
β-strand	347-353	7	19
β-strand	361-363	3	20
β-strand	376-379	4	20
α-helix	382-384	3
β-strand	386-388	3	20
β-strand	715-716	2	20
β-strand	720-727	8	21
β-strand	732-742	11	21
β-strand	750-751	2	21
α-helix	757-759	3
β-strand	763-765	3	21
β-strand	785-795	11	21
β-strand	801-806	6	21
β-strand	811-819	9	22
β-strand	828-835	8	22
β-strand	847-851	5	22
β-strand	854	1	23
β-strand	857	1	23
β-strand	860-865	6	22
β-strand	872-876	5	24
β-strand	879-883	5	24
β-strand	888-893	6	24
β-strand	899-901	3	24
β-strand	911-917	7	25
β-strand	920-925	6	25
β-strand	930-936	7	25
β-strand	941-947	7	25
β-strand	954-959	6	26
β-strand	964-969	6	26
β-strand	973-979	7	26
β-strand	991	1	25
β-strand	992-998	7	26
β-strand	1004-1009	6	10
β-strand	1025-1032	8	10
β-strand	1037-1042	6	10
α-helix	1045-1058	14
α-helix	1070-1074	5
β-strand	1076-1077	2	27
β-strand	1082-1083	2	27
β-strand	1086	1	26
β-strand	1090	1	10
α-helix	1091-1096	6
α-helix	1097-1099	3
α-helix	1102-1108	7
β-strand	1114-1115	2	28
β-strand	1121-1122	2	28
α-helix	1131-1135	5

Chain F: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	11
α-helix	40-42	3
β-strand	46-49	4	15
α-helix	56-62	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DET1 homolog	A	protein	550	Homo sapiens	Q7L5Y6 (AlphaFold model)
DNA damage-binding protein 1	B	protein	1140	Homo sapiens	Q16531 (AlphaFold model)
DET1- and DDB1-associated protein 1	F	protein	102	Homo sapiens	Q9BW61 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9LTJ_1 DET1 homolog (chains A)
MDHHVSTIKPRRIQNQNVIHRLERRRISSGKAGTHWHQVRVFHQNVFPNFTVVNVEKPPC
FLRKFSPDGRYFIAFSSDQTSLEIYEYQGCQAAEDLLQGYEGEILSNGNDQRSVNIRGRL
FERFFVLLHITNVAANGEHLNRECSLFTDDCRCVIVGSAAYLPDEPHPPFFEVYRNSESV
TPNPRSPLEDYSLHIIDLHTGRLCDTRTFKCDKVVLSHNQGLYLYKNILAILSVQQQTIH
VFQVTPEGTFIDVRTIGRFCYEDDLLTVSAVFPEVQRDSQTGMANPFRDPFINSLKHRLL
VYLWRRAEQDGSAMAKRRFFQYFDQLRQLRMWKMQLLDENHLFIKYTSEDVVTLRVTDPS
QASFFVVYNMVTTEVIAVFENTSDELLELFENFCDLFRNATLHSEVQFPCSASSNNFARQ
IQRRFKDTIINAKYGGHTEAVRRLLGQLPISAQSYSGSPYLDLSLFSYDDKWVSVMERPK
TCGDHPIRFYARDSGLLKFEIQAGLLGRPINHTVRRLVAFTFHPFEPFAISVQRTNAEYV
VNFHMRHCCT

Sequence of entity 2 (B), FASTA

>9LTJ_2 DNA damage-binding protein 1 (chains B)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 3 (F), FASTA

>9LTJ_3 DET1- and DDB1-associated protein 1 (chains F)
MADFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLH
QQWDKKNAAKKRDQEQVELEGESSAPPRKVARTDSPDMHEDT

Primary citation

Cryo-EM structure of the human COP1-DET1 ubiquitin ligase complex. Wang, S., Teng, F., Stjepanovic, G. et al. Nat Commun (2026) 17:543-543. DOI 10.1038/s41467-026-68375-7 · PubMed

Other PDB entries of the same protein (UniProt Q7L5Y6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BJZ 2.83 Å, Structure of the human DDD-Ube2e2 complex
9DHD 2.9 Å, The ternary complex of DDB1, DDA1, DET1
9LTO 2.92 Å, Cryo-EM structure of DDB1-DDA1-DET1-Ube2e2 complex
9LTL 2.93 Å, Cryo-EM structure of DDB1-DDA1-DET1 complex
9LTR 3.03 Å, Cryo-EM structure of dimeric DDB1-DDA1-DET1-Ube2e2-COP1 complex
9LTW 3.25 Å, protein structure of DDB1-DDA1-DET1
9LTZ 3.26 Å, protein structure of DDB1-DDA1-DET1-Ube2e2 complex
9LU1 3.62 Å, protein structure of DDB1-DDA1-DET1-Ube2e2 bound to COP1 dimer
9W90 3.7 Å, DDB1-DDA1-DET1-Ube2e2-COP1-c-Jun-STK40 complex
9M0Y 4.25 Å, Local refinement of stacked like DDB1-DDA1-DET1-Ube2e2-COP1 complex (layer 2)
9LUL 4.99 Å, Local refinement of stacked like DDB1-DDA1-DET1-Ube2e2-COP1 complex (layer 1)

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