9LTW: Protein structure of DDB1-DDA1-DET1

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

protein structure of DDB1-DDA1-DET1. Determined by electron microscopy at 3.25 Å resolution. Released 28 Jan 2026.

Method: Electron microscopy
Resolution: 3.25 Å
Organism: Homo sapiens
Chains: 3
Atoms: 8,004
Mol. weight: 202.88 kDa
Released: 28 Jan 2026

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

Secondary structure: helices and β-sheets

9LTW contains 23 α-helices and 94 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, 23 β-strands

Element	Residues	Length	Sheet
α-helix	18-25	8
α-helix	35-39	5
α-helix	40-44	5
β-strand	61-65	5	1
β-strand	71-75	5	1
β-strand	82-86	5	1
α-helix	121-124	4
β-strand	127-129	3	1
β-strand	139-147	9	2
β-strand	154-159	6	2
β-strand	192-196	5	2
β-strand	203-206	4	2
β-strand	228-229	2	3
β-strand	241-244	4	3
β-strand	250-254	5	3
β-strand	330-331	2	4
β-strand	342	1	5
β-strand	346-347	2	4
β-strand	367-369	3	5
β-strand	374-377	4	5
α-helix	459-461	3
β-strand	466-467	2	6
β-strand	488	1	7
β-strand	490-491	2	6
β-strand	500	1	7
β-strand	521-522	2	8
β-strand	529-532	4	8
β-strand	541-543	3	8

Chain B: 15 helices, 70 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	9
β-strand	17-21	5	10
β-strand	30-35	6	10
β-strand	38-45	8	10
β-strand	48-56	9	10
β-strand	61-67	7	11
β-strand	76-81	6	11
β-strand	85-94	10	11
β-strand	97-107	11	11
α-helix	114	1
β-strand	115	1	12
α-helix	116	1
β-strand	121-124	4	13
β-strand	130-134	5	13
β-strand	136	1	12
β-strand	139-144	6	13
β-strand	151-154	4	11
β-strand	155-158	4	13
β-strand	164-169	6	14
α-helix	170	1
β-strand	177-184	8	14
β-strand	187-194	8	14
β-strand	203-204	2	14
β-strand	212	1	14
β-strand	218-221	4	15
β-strand	229-232	4	15
β-strand	237-241	5	15
β-strand	244-248	5	15
α-helix	253-255	3
β-strand	258-263	6	16
β-strand	270	1	17
β-strand	271-275	5	16
β-strand	279-289	11	17
β-strand	295-307	13	17
α-helix	310-311	2
β-strand	313-316	4	18
β-strand	321-325	5	18
β-strand	331-336	6	18
β-strand	347-353	7	18
α-helix	357-359	3
β-strand	362-363	2	19
β-strand	376-379	4	19
α-helix	382-384	3
β-strand	386-388	3	19
β-strand	715-716	2	19
β-strand	721-727	7	20
β-strand	732-737	6	20
β-strand	740-742	3	21
β-strand	750-751	2	21
β-strand	763-765	3	20
β-strand	786-787	2	21
β-strand	790-795	6	20
β-strand	801-806	6	20
β-strand	811	1	22
β-strand	815-819	5	23
β-strand	828-832	5	23
β-strand	835	1	22
β-strand	848-854	7	23
β-strand	857-862	6	23
β-strand	870-876	7	24
β-strand	879-884	6	24
β-strand	887-893	7	24
β-strand	899-905	7	24
β-strand	913-917	5	25
β-strand	920-924	5	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	992-998	7	26
β-strand	1004-1009	6	9
β-strand	1025-1032	8	9
β-strand	1037-1042	6	9
α-helix	1045-1058	14
α-helix	1063-1064	2
α-helix	1070-1073	4
β-strand	1090	1	9
α-helix	1091-1096	6
α-helix	1097-1099	3
α-helix	1102-1105	4
β-strand	1114	1	27
β-strand	1122	1	27
α-helix	1128-1130	3
α-helix	1132-1135	4

Chain F: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	41-43	3
β-strand	45-49	5	11
α-helix	56-59	4
α-helix	61-63	3

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

>9LTW_1 DET1 homolog (chains A)
MDHHVSTIKPRRIQNQNVIHRLERRRISSGKAGTHWHQVRVFHQNVFPNFTVVNVEKPPC
FLRKFSPDGRYFIAFSSDQTSLEIYEYQGCQAAEDLLQGYEGEILSNGNDQRSVNIRGRL
FERFFVLLHITNVAANGEHLNRECSLFTDDCRCVIVGSAAYLPDEPHPPFFEVYRNSESV
TPNPRSPLEDYSLHIIDLHTGRLCDTRTFKCDKVVLSHNQGLYLYKNILAILSVQQQTIH
VFQVTPEGTFIDVRTIGRFCYEDDLLTVSAVFPEVQRDSQTGMANPFRDPFINSLKHRLL
VYLWRRAEQDGSAMAKRRFFQYFDQLRQLRMWKMQLLDENHLFIKYTSEDVVTLRVTDPS
QASFFVVYNMVTTEVIAVFENTSDELLELFENFCDLFRNATLHSEVQFPCSASSNNFARQ
IQRRFKDTIINAKYGGHTEAVRRLLGQLPISAQSYSGSPYLDLSLFSYDDKWVSVMERPK
TCGDHPIRFYARDSGLLKFEIQAGLLGRPINHTVRRLVAFTFHPFEPFAISVQRTNAEYV
VNFHMRHCCT

Sequence of entity 2 (B), FASTA

>9LTW_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

>9LTW_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
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
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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