9LTR: Dimeric DDB1-DDA1-DET1-Ube2e2-COP1 complex

Name: PDB 9LTR: Cryo-EM structure of dimeric DDB1-DDA1-DET1-Ube2e2-COP1 complex
Published: 2026-01-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Cryo-EM structure of dimeric DDB1-DDA1-DET1-Ube2e2-COP1 complex. Determined by electron microscopy at 3.03 Å resolution. Released 28 Jan 2026.

Method: Electron microscopy
Resolution: 3.03 Å
Organism: Homo sapiens
Chains: 10
Atoms: 21,139
Mol. weight: 611.47 kDa
Released: 28 Jan 2026

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

Secondary structure: helices and β-sheets

9LTR contains 89 α-helices and 336 β-strands across 10 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: 1 helix, 31 β-strands

Element	Residues	Length	Sheet
β-strand	411-412	2	1
β-strand	424-429	6	2
β-strand	436-440	5	2
β-strand	444-447	4	2
α-helix	450-455	6
β-strand	465-468	4	2
β-strand	473-478	6	3
β-strand	485-490	6	3
β-strand	495-499	5	3
β-strand	505-507	3	3
β-strand	516	1	4
β-strand	520-521	2	5
β-strand	528-530	3	5
β-strand	533	1	4
β-strand	537	1	6
β-strand	540-542	3	5
β-strand	548-550	3	5
β-strand	553	1	6
β-strand	558-562	5	7
β-strand	572-575	4	7
β-strand	579-582	4	7
β-strand	593-596	4	7
β-strand	602-605	4	8
β-strand	615-617	3	8
β-strand	621-622	2	8
β-strand	648-650	3	9
β-strand	654-657	4	9
β-strand	663-668	6	9
β-strand	676-679	4	9
β-strand	700-705	6	1
β-strand	716-720	5	1
β-strand	724-726	3	1

Chain B: 11 helices, 106 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	10
β-strand	17-21	5	11
β-strand	30-34	5	11
β-strand	39-43	5	11
β-strand	50-55	6	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
β-strand	115	1	13
β-strand	122-124	3	13
β-strand	130-136	7	13
β-strand	139-144	6	13
β-strand	153-154	2	14
β-strand	155-158	4	13
α-helix	159	1
β-strand	164-169	6	15
β-strand	178-183	6	15
β-strand	188-193	6	15
β-strand	196	1	16
β-strand	201	1	16
β-strand	211	1	15
β-strand	216-221	6	17
β-strand	229-233	5	17
β-strand	237-241	5	17
β-strand	244-248	5	17
α-helix	252-255	4
β-strand	261-263	3	18
β-strand	270-274	5	18
β-strand	279-285	7	18
β-strand	288-289	2	19
β-strand	295-296	2	19
β-strand	300-307	8	18
β-strand	311-318	8	20
β-strand	321-326	6	20
β-strand	331-336	6	20
β-strand	342	1	21
β-strand	345	1	21
β-strand	347-353	7	20
β-strand	361-363	3	22
β-strand	375-379	5	22
α-helix	382-384	3
β-strand	386-391	6	22
β-strand	396-403	8	23
β-strand	410-413	4	24
β-strand	424-427	4	24
β-strand	437	1	25
β-strand	444	1	25
β-strand	460-463	4	26
β-strand	467-470	4	26
β-strand	476-480	5	26
β-strand	486-490	5	26
β-strand	498-503	6	27
β-strand	507-512	6	27
β-strand	515-522	8	27
β-strand	525-533	9	27
β-strand	538-541	4	28
β-strand	555	1	29
β-strand	558-560	3	28
β-strand	568-569	2	30
β-strand	570	1	29
β-strand	576-578	3	30
α-helix	586-587	2
β-strand	588-594	7	31
β-strand	601-606	6	31
β-strand	610-615	6	31
β-strand	626-630	5	31
β-strand	637-642	6	32
β-strand	647-652	6	32
β-strand	657-661	5	32
β-strand	666-670	5	32
β-strand	676-684	9	23
β-strand	687-695	9	23
β-strand	698-704	7	23
β-strand	711-715	5	22
β-strand	724-727	4	33
β-strand	732-741	10	33
β-strand	786-795	10	33
β-strand	801-803	3	33
β-strand	806	1	33
β-strand	811-813	3	34
β-strand	817-820	4	35
β-strand	827-831	5	35
β-strand	833-835	3	34
β-strand	845	1	36
β-strand	849-853	5	35
β-strand	858-863	6	35
β-strand	867	1	36
β-strand	872	1	37
β-strand	875	1	38
β-strand	880	1	38
β-strand	883-884	2	37
β-strand	887-893	7	37
β-strand	899-905	7	37
β-strand	911-916	6	39
β-strand	920-925	6	39
β-strand	930-935	6	39
β-strand	942-947	6	39
β-strand	964	1	40
β-strand	967-968	2	41
β-strand	973-976	4	41
β-strand	978	1	40
β-strand	996-999	4	41
β-strand	1004-1009	6	42
β-strand	1028-1032	5	42
β-strand	1038-1042	5	10
α-helix	1045-1061	17
α-helix	1070-1073	4
β-strand	1076	1	43
β-strand	1083	1	43
β-strand	1086	1	41
β-strand	1088-1090	3	10
α-helix	1091-1094	4
α-helix	1095-1099	5
α-helix	1123-1125	3
α-helix	1128-1136	9
α-helix	1137-1139	3

Chain C: 1 helix, 30 β-strands

Element	Residues	Length	Sheet
β-strand	411-412	2	44
β-strand	424-429	6	45
β-strand	435-440	6	45
β-strand	444-449	6	45
α-helix	451-455	5
β-strand	465-468	4	45
β-strand	475-478	4	46
β-strand	485-489	5	46
β-strand	495-499	5	46
β-strand	505-507	3	46
β-strand	516	1	47
β-strand	520-521	2	48
β-strand	529-531	3	48
β-strand	533	1	47
β-strand	537-541	5	48
β-strand	548-553	6	48
β-strand	558-563	6	49
β-strand	570-575	6	49
β-strand	579-584	6	49
β-strand	594-596	3	49
β-strand	602-606	5	50
β-strand	614-617	4	50
β-strand	648-650	3	51
β-strand	654-659	6	51
β-strand	663-668	6	51
β-strand	676-679	4	51
β-strand	683	1	52
β-strand	692	1	52
β-strand	700-703	4	44
β-strand	718-720	3	44
β-strand	724-726	3	44

Chain D: 25 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	18-27	10
α-helix	29-31	3
α-helix	35-40	6
α-helix	41-44	4
β-strand	52-55	4	53
β-strand	60-65	6	54
β-strand	71-76	6	54
β-strand	81-87	7	54
α-helix	92-94	3
β-strand	105	1	53
α-helix	113-124	12
β-strand	125-132	8	54
β-strand	138-140	3	55
β-strand	146-147	2	55
β-strand	153-161	9	55
α-helix	162-163	2
α-helix	167-169	3
α-helix	170-172	3
α-helix	181-183	3
β-strand	189-197	9	55
β-strand	203-212	10	55
α-helix	217-219	3
β-strand	222-225	4	56
β-strand	228-233	6	56
β-strand	238-245	8	56
β-strand	249-256	8	56
α-helix	264-271	8
α-helix	292-293	2
α-helix	294-310	17
α-helix	313-321	9
α-helix	323-326	4
β-strand	330-335	6	57
β-strand	341-347	7	57
α-helix	349-352	4
β-strand	364-369	6	57
β-strand	374-380	7	57
α-helix	384-391	8
α-helix	394-398	5
α-helix	417-430	14
α-helix	437-445	9
α-helix	448	1
α-helix	450	1
β-strand	455	1	58
β-strand	466-467	2	59
β-strand	476	1	58
β-strand	480-481	2	53
α-helix	486	1
β-strand	487-491	5	59
β-strand	497-501	5	59
α-helix	515-516	2
β-strand	517-520	4	53
β-strand	529-535	7	53
β-strand	538-544	7	53

Chain E: 11 helices, 98 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	60
β-strand	17-21	5	61
β-strand	30-34	5	61
β-strand	39-45	7	61
β-strand	48-55	8	61
β-strand	63-67	5	62
β-strand	76-80	5	62
β-strand	85-94	10	62
β-strand	97-107	11	62
β-strand	115	1	63
β-strand	122-124	3	63
β-strand	130-133	4	63
β-strand	136	1	63
β-strand	139-144	6	63
β-strand	153-154	2	64
β-strand	155-158	4	63
α-helix	159	1
β-strand	164-169	6	65
β-strand	177-183	7	65
β-strand	188-196	9	65
β-strand	201-204	4	65
β-strand	211	1	65
β-strand	216-221	6	66
β-strand	229-233	5	66
β-strand	237-241	5	66
β-strand	244-248	5	66
α-helix	252-255	4
β-strand	261-263	3	67
β-strand	270-274	5	67
β-strand	279-289	11	67
β-strand	295-307	13	67
β-strand	314-318	5	68
β-strand	321-324	4	68
β-strand	331-336	6	68
β-strand	347-353	7	68
β-strand	362-363	2	69
β-strand	375-381	7	69
β-strand	384-390	7	69
β-strand	394	1	70
β-strand	396-403	8	71
β-strand	410-413	4	72
β-strand	424-427	4	72
β-strand	437	1	73
β-strand	444	1	73
β-strand	459-463	5	74
β-strand	467-471	5	74
β-strand	475-480	6	74
β-strand	486-491	6	74
β-strand	500-502	3	75
β-strand	507-512	6	75
β-strand	515-522	8	75
β-strand	525-533	9	75
β-strand	538-541	4	76
β-strand	555	1	77
β-strand	558-560	3	76
β-strand	568	1	78
β-strand	570	1	77
β-strand	578	1	78
α-helix	586-587	2
β-strand	588-594	7	79
β-strand	601-606	6	79
β-strand	610-615	6	79
β-strand	627-630	4	79
β-strand	637-642	6	80
β-strand	647-652	6	80
β-strand	657-661	5	80
β-strand	666-670	5	80
β-strand	671	1	70
β-strand	678-682	5	71
β-strand	690-694	5	71
β-strand	698-704	7	71
β-strand	712-715	4	69
β-strand	725-727	3	81
β-strand	732-741	10	81
β-strand	786-795	10	81
β-strand	801-806	6	81
β-strand	811-813	3	82
β-strand	817-820	4	83
β-strand	827-831	5	83
β-strand	833-835	3	82
β-strand	849-853	5	83
β-strand	858-863	6	83
β-strand	872	1	84
β-strand	883-884	2	84
β-strand	887-893	7	84
β-strand	899-905	7	84
β-strand	915-916	2	85
β-strand	920-924	5	85
β-strand	930-934	5	85
β-strand	935-936	2	86
β-strand	941-942	2	86
β-strand	946-947	2	85
β-strand	967-968	2	87
β-strand	973-976	4	87
α-helix	978-980	3
β-strand	996-999	4	87
β-strand	1004-1007	4	88
β-strand	1028-1029	2	89
β-strand	1030-1032	3	88
β-strand	1038	1	60
β-strand	1039-1040	2	89
α-helix	1045-1061	17
β-strand	1086	1	87
α-helix	1091-1094	4
α-helix	1095-1099	5
α-helix	1107-1109	3
α-helix	1123-1125	3
α-helix	1128-1136	9
α-helix	1137-1139	3

Chain H: 23 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
α-helix	18-27	10
α-helix	35-40	6
α-helix	41-44	4
β-strand	52-55	4	90
β-strand	60-65	6	91
β-strand	71-76	6	91
β-strand	81-87	7	91
α-helix	92-94	3
β-strand	105	1	90
α-helix	111-124	14
β-strand	125-132	8	91
β-strand	138-147	10	92
β-strand	154-161	8	92
α-helix	162-163	2
α-helix	167-169	3
α-helix	170-173	4
α-helix	181-183	3
β-strand	189-196	8	92
β-strand	203-212	10	92
α-helix	217-219	3
β-strand	222-225	4	93
β-strand	228-233	6	93
β-strand	238-245	8	93
β-strand	249-256	8	93
α-helix	264-271	8
α-helix	273-281	9
α-helix	294-310	17
α-helix	313-321	9
α-helix	323-328	6
β-strand	330-335	6	94
β-strand	341-347	7	94
α-helix	349-352	4
β-strand	364-369	6	94
β-strand	374-380	7	94
α-helix	384-391	8
α-helix	394-398	5
α-helix	417-430	14
α-helix	437-445	9
α-helix	448	1
α-helix	450	1
β-strand	455	1	95
β-strand	466-467	2	96
β-strand	476	1	95
β-strand	480-481	2	90
β-strand	487-491	5	96
β-strand	497-501	5	96
β-strand	517-520	4	90
β-strand	529-534	6	90
β-strand	539-544	6	90

Chain I: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	61
α-helix	41-43	3
β-strand	48-49	2	64
α-helix	57-60	4

Chain J: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	55-69	15
α-helix	71-72	2
β-strand	76-79	4	97
β-strand	86-92	7	97
α-helix	93-94	2
β-strand	103-109	7	97
α-helix	118-119	2
β-strand	120-123	4	97
β-strand	132	1	98
β-strand	137	1	97
β-strand	138	1	98
α-helix	153-165	13
α-helix	175-183	9
α-helix	185-198	14

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase COP1	A, C	protein	731	Homo sapiens	Q8NHY2 (AlphaFold model)
DNA damage-binding protein 1	B, E	protein	1140	Homo sapiens	Q16531 (AlphaFold model)
DET1 homolog	D, H	protein	550	Homo sapiens	Q7L5Y6 (AlphaFold model)
DET1- and DDB1-associated protein 1	I, P	protein	102	Homo sapiens	Q9BW61 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 E2	J, K	protein	201	Homo sapiens	Q96LR5

Sequence of entity 1 (A, C), FASTA

>9LTR_1 E3 ubiquitin-protein ligase COP1 (chains A, C)
MSGSRQAGSGSAGTSPGSSAASSVTSASSSLSSSPSPPSVAVSAAALVSGGVAQAAGSGG
LGGPVRPVLVAPAVSGSGGGAVSTGLSRHSCAARPSAGVGGSSSSLGSGSRKRPLLAPLC
NGLINSYEDKSNDFVCPICFDMIEEAYMTKCGHSFCYKCIHQSLEDNNRCPKCNYVVDNI
DHLYPNFLVNELILKQKQRFEEKRFKLDHSVSSTNGHRWQIFQDWLGTDQDNLDLANVNL
MLELLVQKKKQLEAESHAAQLQILMEFLKVARRNKREQLEQIQKELSVLEEDIKRVEEMS
GLYSPVSEDSTVPQFEAPSPSHSSIIDSTEYSQPPGFSGSSQTKKQPWYNSTLASRRKRL
TAHFEDLEQCYFSTRMSRISDDSRTASQLDEFQECLSKFTRYNSVRPLATLSYASDLYNG
SSIVSSIEFDRDCDYFAIAGVTKKIKVYEYDTVIQDAVDIHYPENEMTCNSKISCISWSS
YHKNLLASSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFNLMDPKLLASGSDDAKVKL
WSTNLDNSVASIEAKANVCCVKFSPSSRYHLAFGCADHCVHYYDLRNTKQPIMVFKGHRK
AVSYAKFVSGEEIVSASTDSQLKLWNVGKPYCLRSFKGHINEKNFVGLASNGDYIACGSE
NNSLYLYYKGLSKTLLTFKFDTVKSVLDKDRKEDDTNEFVSAVCWRALPDGESNVLIAAN
SQGTIKVLELV

Sequence of entity 2 (B, E), FASTA

>9LTR_2 DNA damage-binding protein 1 (chains B, E)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 3 (D, H), FASTA

>9LTR_3 DET1 homolog (chains D, H)
MDHHVSTIKPRRIQNQNVIHRLERRRISSGKAGTHWHQVRVFHQNVFPNFTVVNVEKPPC
FLRKFSPDGRYFIAFSSDQTSLEIYEYQGCQAAEDLLQGYEGEILSNGNDQRSVNIRGRL
FERFFVLLHITNVAANGEHLNRECSLFTDDCRCVIVGSAAYLPDEPHPPFFEVYRNSESV
TPNPRSPLEDYSLHIIDLHTGRLCDTRTFKCDKVVLSHNQGLYLYKNILAILSVQQQTIH
VFQVTPEGTFIDVRTIGRFCYEDDLLTVSAVFPEVQRDSQTGMANPFRDPFINSLKHRLL
VYLWRRAEQDGSAMAKRRFFQYFDQLRQLRMWKMQLLDENHLFIKYTSEDVVTLRVTDPS
QASFFVVYNMVTTEVIAVFENTSDELLELFENFCDLFRNATLHSEVQFPCSASSNNFARQ
IQRRFKDTIINAKYGGHTEAVRRLLGQLPISAQSYSGSPYLDLSLFSYDDKWVSVMERPK
TCGDHPIRFYARDSGLLKFEIQAGLLGRPINHTVRRLVAFTFHPFEPFAISVQRTNAEYV
VNFHMRHCCT

Sequence of entity 4 (I, P), FASTA

>9LTR_4 DET1- and DDB1-associated protein 1 (chains I, P)
MADFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLH
QQWDKKNAAKKRDQEQVELEGESSAPPRKVARTDSPDMHEDT

Sequence of entity 5 (J, K), FASTA

>9LTR_5 Ubiquitin-conjugating enzyme E2 E2 (chains J, K)
MSTEAQRVDDSPSTSGGSSDGDQRESVQQEPEREQVQPKKKEGKISSKTAAKLSTSAKRI
QKELAEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSPDYPFKPPK
VTFRTRIYHCNINSQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQ
YMTNRAEHDRMARQWTKRYAT

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 Q8NHY2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5HQG 2.0 Å, WD40 domain of Human E3 Ubiquitin Ligase COP1 (RFWD2)
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
5IGQ 3.9 Å, WD40 domain of Human E3 Ubiquitin Ligase COP1 (RFWD2) bound to peptide from Trib1
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)

Browse structure collections

About this viewer

MolViewer shows 9LTR directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.