9LTO: DDB1-DDA1-DET1-Ube2e2 complex

Name: PDB 9LTO: Cryo-EM structure of DDB1-DDA1-DET1-Ube2e2 complex
Published: 2026-01-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Cryo-EM structure of DDB1-DDA1-DET1-Ube2e2 complex. Determined by electron microscopy at 2.92 Å resolution. Released 28 Jan 2026.

Method: Electron microscopy
Resolution: 2.92 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,873
Mol. weight: 225.17 kDa
Released: 28 Jan 2026

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

Secondary structure: helices and β-sheets

9LTO contains 35 α-helices and 112 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: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	61-69	9
α-helix	71-72	2
β-strand	76-79	4	1
β-strand	86-92	7	1
α-helix	93-94	2
β-strand	103-109	7	1
β-strand	122	1	1
β-strand	137	1	1
α-helix	153-165	13
α-helix	175-183	9
α-helix	185-199	15

Chain B: 20 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	18-25	8
α-helix	35-40	6
α-helix	41-44	4
β-strand	50-52	3	23
β-strand	61-65	5	24
β-strand	71-75	5	24
β-strand	81-87	7	24
β-strand	104-105	2	23
α-helix	111-124	14
β-strand	125-132	8	24
β-strand	139-140	2	25
β-strand	146-147	2	26
β-strand	153-157	5	26
β-strand	158-159	2	25
β-strand	161	1	26
α-helix	170-173	4
β-strand	189-197	9	26
β-strand	203-212	10	26
α-helix	217-219	3
β-strand	222-225	4	27
β-strand	228-233	6	27
β-strand	238-244	7	27
β-strand	250-256	7	27
α-helix	264-271	8
α-helix	286-288	3
α-helix	292-293	2
α-helix	294-310	17
α-helix	313-319	7
α-helix	323-327	5
β-strand	329-336	8	28
β-strand	341-348	8	28
α-helix	349-352	4
β-strand	364-369	6	28
β-strand	374	1	28
β-strand	378-379	2	28
α-helix	384-392	9
α-helix	394-398	5
α-helix	416-430	15
α-helix	437-445	9
α-helix	448	1
α-helix	450-451	2
β-strand	455	1	29
β-strand	466-468	3	30
β-strand	476	1	29
β-strand	480-481	2	23
α-helix	486	1
β-strand	487-491	5	30
β-strand	497-501	5	30
β-strand	517-522	6	23
β-strand	528-534	7	23
β-strand	539-545	7	23

Chain D: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	46	1	7
β-strand	49	1	8
α-helix	54-66	13

Chain S: 8 helices, 74 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	2
β-strand	17-21	5	3
β-strand	30-34	5	3
β-strand	39-43	5	3
β-strand	50-55	6	3
β-strand	61-67	7	4
β-strand	76-81	6	4
β-strand	85-92	8	4
β-strand	99-107	9	4
β-strand	115	1	5
β-strand	121-124	4	6
β-strand	130-134	5	6
β-strand	136	1	5
β-strand	139-144	6	6
β-strand	151	1	7
β-strand	154	1	8
β-strand	155-158	4	6
β-strand	164-169	6	9
β-strand	177-184	8	9
β-strand	187-189	3	9
β-strand	192-196	5	9
β-strand	201-204	4	9
β-strand	218-221	4	10
β-strand	229-232	4	10
β-strand	237-239	3	10
β-strand	246-248	3	10
β-strand	258-263	6	11
β-strand	270-275	6	11
β-strand	279-289	11	11
β-strand	295-302	8	11
β-strand	306-307	2	11
β-strand	315-316	2	12
β-strand	322-324	3	12
β-strand	331-334	4	12
β-strand	349-353	5	12
β-strand	362	1	13
β-strand	377	1	13
β-strand	379	1	14
α-helix	382-384	3
β-strand	386	1	14
β-strand	716	1	14
β-strand	720-727	8	15
β-strand	732-743	12	15
β-strand	748-749	2	15
β-strand	762-765	4	15
β-strand	785-794	10	15
β-strand	801-806	6	15
β-strand	811	1	16
β-strand	815-819	5	17
β-strand	828-834	7	17
β-strand	835	1	16
β-strand	846-854	9	17
β-strand	857-866	10	17
β-strand	870-876	7	18
β-strand	879-884	6	18
β-strand	888-893	6	18
β-strand	899-905	7	18
β-strand	911-917	7	19
β-strand	920-925	6	19
β-strand	930-936	7	19
β-strand	941-947	7	19
β-strand	954-959	6	20
β-strand	964-969	6	20
β-strand	973-979	7	20
β-strand	991	1	19
β-strand	992-999	8	20
β-strand	1004-1009	6	2
β-strand	1025-1032	8	2
β-strand	1037-1042	6	2
α-helix	1045-1058	14
α-helix	1063-1064	2
α-helix	1070-1073	4
β-strand	1076-1077	2	21
β-strand	1082-1083	2	21
β-strand	1086	1	20
β-strand	1090	1	2
α-helix	1091-1096	6
α-helix	1097-1099	3
α-helix	1102-1106	5
β-strand	1113-1114	2	22
β-strand	1122-1123	2	22
α-helix	1126-1131	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 E2	A	protein	201	Homo sapiens	Q96LR5 (AlphaFold model)
DNA damage-binding protein 1	S	protein	1140	Homo sapiens	Q16531 (AlphaFold model)
DET1 homolog	B	protein	550	Homo sapiens	Q7L5Y6 (AlphaFold model)
DET1- and DDB1-associated protein 1	D	protein	102	Homo sapiens	Q9BW61 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9LTO_1 Ubiquitin-conjugating enzyme E2 E2 (chains A)
MSTEAQRVDDSPSTSGGSSDGDQRESVQQEPEREQVQPKKKEGKISSKTAAKLSTSAKRI
QKELAEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSPDYPFKPPK
VTFRTRIYHCNINSQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQ
YMTNRAEHDRMARQWTKRYAT

Sequence of entity 2 (S), FASTA

>9LTO_2 DNA damage-binding protein 1 (chains S)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 3 (B), FASTA

>9LTO_3 DET1 homolog (chains B)
MDHHVSTIKPRRIQNQNVIHRLERRRISSGKAGTHWHQVRVFHQNVFPNFTVVNVEKPPC
FLRKFSPDGRYFIAFSSDQTSLEIYEYQGCQAAEDLLQGYEGEILSNGNDQRSVNIRGRL
FERFFVLLHITNVAANGEHLNRECSLFTDDCRCVIVGSAAYLPDEPHPPFFEVYRNSESV
TPNPRSPLEDYSLHIIDLHTGRLCDTRTFKCDKVVLSHNQGLYLYKNILAILSVQQQTIH
VFQVTPEGTFIDVRTIGRFCYEDDLLTVSAVFPEVQRDSQTGMANPFRDPFINSLKHRLL
VYLWRRAEQDGSAMAKRRFFQYFDQLRQLRMWKMQLLDENHLFIKYTSEDVVTLRVTDPS
QASFFVVYNMVTTEVIAVFENTSDELLELFENFCDLFRNATLHSEVQFPCSASSNNFARQ
IQRRFKDTIINAKYGGHTEAVRRLLGQLPISAQSYSGSPYLDLSLFSYDDKWVSVMERPK
TCGDHPIRFYARDSGLLKFEIQAGLLGRPINHTVRRLVAFTFHPFEPFAISVQRTNAEYV
VNFHMRHCCT

Sequence of entity 4 (D), FASTA

>9LTO_4 DET1- and DDB1-associated protein 1 (chains D)
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 Q96LR5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1Y6L 1.85 Å, Human ubiquitin conjugating enzyme E2E2
6W9A 2.3 Å, RNF12 RING domain in complex with Ube2e2
9BJZ 2.83 Å, Structure of the human DDD-Ube2e2 complex
9LTR 3.03 Å, Cryo-EM structure of dimeric DDB1-DDA1-DET1-Ube2e2-COP1 complex
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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