9LTL: DDB1-DDA1-DET1 complex

Name: PDB 9LTL: 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 2.93 Å resolution. Released 28 Jan 2026.

Method: Electron microscopy
Resolution: 2.93 Å
Organism: Homo sapiens
Chains: 3
Atoms: 8,055
Mol. weight: 202.88 kDa
Released: 28 Jan 2026

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

Secondary structure: helices and β-sheets

9LTL contains 18 α-helices and 104 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: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	18-27	10
α-helix	40-44	5
β-strand	52-53	2	1
β-strand	65	1	2
β-strand	71-75	5	2
β-strand	82-86	5	2
β-strand	87	1	3
α-helix	121-124	4
β-strand	125	1	3
β-strand	129	1	2
β-strand	145-147	3	4
β-strand	154-158	5	4
β-strand	190	1	5
β-strand	192-196	5	4
β-strand	205-207	3	4
β-strand	211	1	5
β-strand	224	1	6
β-strand	229	1	6
α-helix	234-236	3
β-strand	240-241	2	7
β-strand	244	1	8
β-strand	250	1	8
β-strand	254-255	2	7
β-strand	341	1	9
β-strand	369	1	9
β-strand	374	1	9
α-helix	459-461	3
β-strand	466-468	3	10
β-strand	489-491	3	10
β-strand	497	1	10
β-strand	518-521	4	1
β-strand	528-534	7	1
β-strand	539-545	7	1

Chain B: 12 helices, 74 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	11
β-strand	7-10	4	12
β-strand	17-21	5	13
β-strand	29-34	6	13
β-strand	38-45	8	13
β-strand	48-56	9	13
β-strand	61-67	7	14
β-strand	76-81	6	14
β-strand	85-94	10	14
β-strand	97-107	11	14
α-helix	114	1
β-strand	115	1	15
α-helix	116	1
β-strand	121-124	4	16
β-strand	131-134	4	16
β-strand	136	1	15
β-strand	139-142	4	16
β-strand	152-154	3	14
β-strand	155-158	4	16
β-strand	164-169	6	17
α-helix	170	1
β-strand	177-184	8	17
β-strand	187-195	9	17
β-strand	202-204	3	17
β-strand	210-212	3	17
β-strand	218-221	4	18
β-strand	229-232	4	18
β-strand	237-241	5	18
β-strand	244-248	5	18
α-helix	253-255	3
β-strand	258-263	6	19
β-strand	270-275	6	19
β-strand	279-288	10	19
β-strand	296-307	12	19
β-strand	313-318	6	20
β-strand	321-325	5	20
β-strand	331-336	6	20
β-strand	347-353	7	20
β-strand	361-363	3	21
β-strand	376-379	4	21
α-helix	382-384	3
β-strand	386-388	3	21
β-strand	715-716	2	21
β-strand	721-727	7	22
β-strand	732-737	6	22
β-strand	740-742	3	23
β-strand	751	1	23
β-strand	763-765	3	22
β-strand	785-787	3	23
β-strand	790-795	6	22
β-strand	801-806	6	22
β-strand	811-819	9	24
β-strand	828-835	8	24
β-strand	846	1	25
β-strand	847-854	8	24
β-strand	857-862	6	24
β-strand	866	1	25
β-strand	870-876	7	26
β-strand	879-884	6	26
β-strand	887-893	7	26
β-strand	899-905	7	26
β-strand	911-917	7	27
β-strand	920-925	6	27
β-strand	930-936	7	27
β-strand	941-947	7	27
β-strand	957-959	3	28
β-strand	964-968	5	28
β-strand	974-978	5	28
β-strand	991	1	27
β-strand	993-997	5	28
β-strand	1004-1009	6	12
β-strand	1028-1032	5	12
β-strand	1037-1040	4	12
α-helix	1045-1061	17
α-helix	1070-1073	4
β-strand	1076-1077	2	29
β-strand	1082-1083	2	29
β-strand	1086	1	28
β-strand	1088-1090	3	11
α-helix	1091-1096	6
α-helix	1097-1099	3
α-helix	1102-1106	5
β-strand	1113-1114	2	30
β-strand	1122-1123	2	30
α-helix	1124-1125	2
α-helix	1132-1135	4

Chain F: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	13
α-helix	41-43	3
β-strand	45-49	5	14

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

>9LTL_1 DET1 homolog (chains A)
MDHHVSTIKPRRIQNQNVIHRLERRRISSGKAGTHWHQVRVFHQNVFPNFTVVNVEKPPC
FLRKFSPDGRYFIAFSSDQTSLEIYEYQGCQAAEDLLQGYEGEILSNGNDQRSVNIRGRL
FERFFVLLHITNVAANGEHLNRECSLFTDDCRCVIVGSAAYLPDEPHPPFFEVYRNSESV
TPNPRSPLEDYSLHIIDLHTGRLCDTRTFKCDKVVLSHNQGLYLYKNILAILSVQQQTIH
VFQVTPEGTFIDVRTIGRFCYEDDLLTVSAVFPEVQRDSQTGMANPFRDPFINSLKHRLL
VYLWRRAEQDGSAMAKRRFFQYFDQLRQLRMWKMQLLDENHLFIKYTSEDVVTLRVTDPS
QASFFVVYNMVTTEVIAVFENTSDELLELFENFCDLFRNATLHSEVQFPCSASSNNFARQ
IQRRFKDTIINAKYGGHTEAVRRLLGQLPISAQSYSGSPYLDLSLFSYDDKWVSVMERPK
TCGDHPIRFYARDSGLLKFEIQAGLLGRPINHTVRRLVAFTFHPFEPFAISVQRTNAEYV
VNFHMRHCCT

Sequence of entity 2 (B), FASTA

>9LTL_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

>9LTL_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:

9LTJ 2.65 Å, Cryo-EM structure of DDB1-DDA1-DET1 complex
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
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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