9LUL: E3 ubiquitin-protein ligase COP1

Name: PDB 9LUL: Local refinement of stacked like DDB1-DDA1-DET1-Ube2e2-COP1 complex (layer 1)
Published: 2026-01-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Local refinement of stacked like DDB1-DDA1-DET1-Ube2e2-COP1 complex (layer 1). Determined by electron microscopy at 4.99 Å resolution. Released 28 Jan 2026.

Method: Electron microscopy
Resolution: 4.99 Å
Organism: Homo sapiens
Chains: 16
Atoms: 35,663
Mol. weight: 981.93 kDa
Released: 28 Jan 2026

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

Secondary structure: helices and β-sheets

9LUL contains 158 α-helices and 460 β-strands across 16 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: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	48-61	14
α-helix	63-64	2
β-strand	67-71	5	67
β-strand	78-84	7	67
α-helix	85-86	2
β-strand	95-101	7	67
β-strand	112-115	4	67
β-strand	124	1	68
β-strand	130	1	68
α-helix	145-157	13
α-helix	167-175	9
α-helix	177-187	11
α-helix	188-192	5

Chain b: 24 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	20-27	8
α-helix	35-40	6
α-helix	41-44	4
β-strand	50	1	107
β-strand	51-52	2	108
β-strand	60-65	6	109
β-strand	72-76	5	109
β-strand	82-87	6	109
α-helix	90-92	3
β-strand	104-105	2	108
α-helix	111-124	14
β-strand	125-131	7	109
α-helix	134-135	2
β-strand	139-140	2	110
β-strand	146-147	2	110
β-strand	153-161	9	110
α-helix	162-163	2
α-helix	167-169	3
α-helix	170-173	4
α-helix	179-182	4
β-strand	183	1	111
β-strand	186	1	111
β-strand	189-197	9	110
β-strand	203-209	7	110
α-helix	217-219	3
β-strand	222-225	4	112
β-strand	228-233	6	112
β-strand	238-244	7	112
β-strand	250-256	7	112
α-helix	264-271	8
α-helix	294-310	17
α-helix	313-326	14
β-strand	330-335	6	113
β-strand	343-347	5	113
α-helix	349-352	4
β-strand	364-368	5	113
β-strand	375-380	6	113
α-helix	384-390	7
α-helix	394-398	5
α-helix	416-431	16
α-helix	437-445	9
α-helix	448	1
α-helix	450-451	2
α-helix	459-461	3
β-strand	481	1	114
α-helix	482-483	2
α-helix	486	1
β-strand	487-488	2	115
β-strand	500-501	2	115
β-strand	517-521	5	114
β-strand	530-534	5	114
β-strand	539-542	4	114
β-strand	545	1	107

Chain c: 15 helices, 69 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	69
β-strand	17-21	5	70
β-strand	30-35	6	70
β-strand	38-44	7	70
β-strand	49-56	8	70
β-strand	57	1	71
β-strand	61-67	7	72
β-strand	76-81	6	72
β-strand	85-94	10	72
β-strand	97-107	11	72
α-helix	114	1
β-strand	115	1	73
α-helix	116	1
β-strand	121-124	4	74
β-strand	130-134	5	74
β-strand	136	1	73
β-strand	139-144	6	74
β-strand	155-158	4	74
β-strand	163-169	7	75
β-strand	177-184	8	75
β-strand	187-196	10	75
β-strand	201-204	4	75
α-helix	208-209	2
β-strand	210-212	3	75
β-strand	216-221	6	76
β-strand	229-233	5	76
β-strand	237-241	5	76
β-strand	244-248	5	76
α-helix	251-255	5
β-strand	258-263	6	77
β-strand	270-275	6	77
β-strand	279-289	11	77
β-strand	295-307	13	77
β-strand	316-318	3	78
β-strand	321-324	4	78
β-strand	331-336	6	78
β-strand	347-353	7	78
β-strand	359-365	7	79
β-strand	374-379	6	79
α-helix	382-384	3
β-strand	386-391	6	79
β-strand	712-716	5	79
β-strand	720-727	8	80
β-strand	732-743	12	80
α-helix	744	1
β-strand	749-751	3	80
β-strand	763-765	3	80
α-helix	780-781	2
β-strand	785-795	11	80
β-strand	801-806	6	80
β-strand	811-819	9	81
β-strand	828-835	8	81
β-strand	846-854	9	81
β-strand	857-866	10	81
β-strand	870-876	7	82
β-strand	879-884	6	82
β-strand	887-893	7	82
β-strand	899-905	7	82
β-strand	913-917	5	83
β-strand	920-924	5	83
β-strand	930-935	6	83
β-strand	942-947	6	83
β-strand	956-959	4	84
β-strand	964-968	5	84
β-strand	974-978	5	84
α-helix	986-990	5
β-strand	991	1	83
α-helix	992	1
β-strand	993-994	2	84
β-strand	1004-1009	6	69
α-helix	1019-1022	4
β-strand	1025-1032	8	69
β-strand	1037-1043	7	69
α-helix	1045-1061	17
β-strand	1065	1	71
α-helix	1070-1073	4
β-strand	1076-1077	2	85
β-strand	1082-1083	2	85
β-strand	1088-1090	3	69
α-helix	1091-1098	8
α-helix	1102-1109	8
β-strand	1113-1114	2	86
β-strand	1122-1123	2	86
α-helix	1126-1139	14

Chain d: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	48-61	14
α-helix	63-64	2
β-strand	67-71	5	87
β-strand	78-84	7	87
α-helix	85-86	2
β-strand	95-101	7	87
β-strand	112-115	4	87
β-strand	124	1	88
β-strand	130	1	88
α-helix	145-157	13
α-helix	167-175	9
α-helix	177-191	15

Chain e: 20 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	18-27	10
α-helix	35-40	6
α-helix	43-45	3
β-strand	50-52	3	116
β-strand	60-65	6	117
β-strand	71-76	6	117
β-strand	81-87	7	117
α-helix	90-92	3
β-strand	104-105	2	116
α-helix	111-124	14
β-strand	125-132	8	117
β-strand	139-140	2	118
β-strand	146-147	2	118
β-strand	153-161	9	118
α-helix	162-163	2
α-helix	167-169	3
α-helix	170-173	4
α-helix	179-182	4
β-strand	183	1	119
β-strand	186	1	119
β-strand	189-197	9	118
β-strand	202-209	8	118
β-strand	222-225	4	120
β-strand	228-233	6	120
β-strand	238-245	8	120
β-strand	249-256	8	120
α-helix	264-271	8
α-helix	273-281	9
α-helix	292-293	2
α-helix	294-310	17
α-helix	313-327	15
β-strand	330-338	9	121
β-strand	341-347	7	121
α-helix	349-352	4
β-strand	364-369	6	121
β-strand	375-380	6	121
α-helix	384-390	7
α-helix	394-398	5
α-helix	416-431	16
α-helix	436-445	10
β-strand	466-467	2	122
β-strand	480-481	2	116
α-helix	486	1
β-strand	487-491	5	122
β-strand	497-501	5	122
β-strand	517-522	6	116
β-strand	529-534	6	116
β-strand	539-545	7	116

Chain f: 16 helices, 70 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	89
β-strand	17-21	5	90
β-strand	30-35	6	90
β-strand	38-44	7	90
β-strand	49-56	8	90
β-strand	61-67	7	91
α-helix	75	1
β-strand	76-81	6	91
β-strand	85-90	6	91
β-strand	93-94	2	92
β-strand	97-98	2	92
β-strand	101-107	7	91
α-helix	114	1
β-strand	115	1	93
α-helix	116	1
β-strand	121-124	4	94
β-strand	130-134	5	94
β-strand	136	1	93
β-strand	139-144	6	94
β-strand	155-158	4	94
β-strand	164-170	7	95
β-strand	177-184	8	95
β-strand	187-196	10	95
β-strand	201-204	4	95
α-helix	208-209	2
β-strand	210-212	3	95
β-strand	216-221	6	96
β-strand	229-233	5	96
β-strand	237-241	5	96
β-strand	244-248	5	96
α-helix	251-254	4
β-strand	258-263	6	97
β-strand	270-275	6	97
β-strand	279-289	11	97
β-strand	295-307	13	97
β-strand	313-316	4	98
β-strand	321-325	5	98
β-strand	331-336	6	98
β-strand	347-353	7	98
β-strand	359-365	7	99
β-strand	374-379	6	99
α-helix	382-384	3
β-strand	386-391	6	99
β-strand	712-716	5	99
β-strand	720-727	8	100
β-strand	732-743	12	100
α-helix	744	1
β-strand	749-751	3	100
β-strand	763-765	3	100
α-helix	780-781	2
β-strand	785-795	11	100
β-strand	801-806	6	100
β-strand	811-819	9	101
β-strand	828-835	8	101
β-strand	845-854	10	101
β-strand	857-866	10	101
β-strand	870-876	7	102
β-strand	879-884	6	102
β-strand	887-893	7	102
β-strand	899-905	7	102
β-strand	913-917	5	103
β-strand	920-924	5	103
β-strand	930-935	6	103
β-strand	942-947	6	103
β-strand	956-959	4	104
β-strand	964-968	5	104
β-strand	973-978	6	104
α-helix	986-990	5
β-strand	991	1	103
α-helix	992	1
β-strand	993-999	7	104
β-strand	1004-1009	6	89
α-helix	1019-1022	4
β-strand	1025-1032	8	89
β-strand	1037-1043	7	89
α-helix	1045-1058	14
α-helix	1070-1074	5
β-strand	1076-1077	2	105
β-strand	1082-1083	2	105
β-strand	1086	1	104
β-strand	1088-1090	3	89
α-helix	1091-1098	8
α-helix	1102-1109	8
β-strand	1113-1115	3	106
β-strand	1121-1123	3	106
α-helix	1126-1139	14

Chain h: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	40-43	4
α-helix	54-65	12

Chain H: 6 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	219-229	11
α-helix	237-283	47
α-helix	348-362	15
α-helix	364-375	12
α-helix	382-399	18
β-strand	405-412	8	1
β-strand	424-429	6	2
β-strand	435-440	6	2
β-strand	444-449	6	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	494-499	6	3
β-strand	505-510	6	3
β-strand	516-521	6	4
β-strand	528-533	6	4
β-strand	537-542	6	4
β-strand	548-553	6	4
β-strand	558-563	6	5
β-strand	570-575	6	5
β-strand	579-584	6	5
β-strand	587-596	10	5
β-strand	602-607	6	6
β-strand	612-617	6	6
β-strand	621-626	6	6
β-strand	632-637	6	6
β-strand	648-651	4	7
β-strand	654-658	5	7
β-strand	664-668	5	7
β-strand	676-678	3	7
β-strand	702-705	4	1
β-strand	715-719	5	1
β-strand	724-730	7	1

8 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	H, I, K, M, N, O, W, X	protein	604	Homo sapiens	Q8NHY2 (AlphaFold model)
DET1- and DDB1-associated protein 1	L, h	protein	66	Homo sapiens	Q9BW61 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 E2	a, d	protein	147	Homo sapiens	Q96LR5 (AlphaFold model)
DNA damage-binding protein 1	c, f	protein	1140	Homo sapiens	Q16531 (AlphaFold model)
DET1 homolog	b, e	protein	542	Homo sapiens	Q7L5Y6

Sequence of entity 1 (H, I, K, M, N, O, W, X), FASTA

>9LUL_1 E3 ubiquitin-protein ligase COP1 (chains H, I, K, M, N, O, W, X)
EDKSNDFVCPICFDMIEEAYMTKCGHSFCYKCIHQSLEDNNRCPKCNYVVDNIDHLYPNF
LVNELILKQKQRFEEKRFKLDHSVSSTNGHRWQIFQDWLGTDQDNLDLANVNLMLELLVQ
KKKQLEAESHAAQLQILMEFLKVARRNKREQLEQIQKELSVLEEDIKRVEEMSGLYSPVS
EDSTVPQFEAPSPSHSSIIDSTEYSQPPGFSGSSQTKKQPWYNSTLASRRKRLTAHFEDL
EQCYFSTRMSRISDDSRTASQLDEFQECLSKFTRYNSVRPLATLSYASDLYNGSSIVSSI
EFDRDCDYFAIAGVTKKIKVYEYDTVIQDAVDIHYPENEMTCNSKISCISWSSYHKNLLA
SSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFNLMDPKLLASGSDDAKVKLWSTNLDN
SVASIEAKANVCCVKFSPSSRYHLAFGCADHCVHYYDLRNTKQPIMVFKGHRKAVSYAKF
VSGEEIVSASTDSQLKLWNVGKPYCLRSFKGHINEKNFVGLASNGDYIACGSENNSLYLY
YKGLSKTLLTFKFDTVKSVLDKDRKEDDTNEFVSAVCWRALPDGESNVLIAANSQGTIKV
LELV

Sequence of entity 2 (L, h), FASTA

>9LUL_2 DET1- and DDB1-associated protein 1 (chains L, h)
ADFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLHQ
QWDKKN

Sequence of entity 3 (a, d), FASTA

>9LUL_3 Ubiquitin-conjugating enzyme E2 E2 (chains a, d)
TSAKRIQKELAEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSPDY
PFKPPKVTFRTRIYHCNINSQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLV
GSIATQYMTNRAEHDRMARQWTKRYAT

Sequence of entity 4 (c, f), FASTA

>9LUL_4 DNA damage-binding protein 1 (chains c, f)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 5 (b, e), FASTA

>9LUL_5 DET1 homolog (chains b, e)
KPRRIQNQNVIHRLERRRISSGKAGTHWHQVRVFHQNVFPNFTVVNVEKPPCFLRKFSPD
GRYFIAFSSDQTSLEIYEYQGCQAAEDLLQGYEGEILSNGNDQRSVNIRGRLFERFFVLL
HITNVAANGEHLNRECSLFTDDCRCVIVGSAAYLPDEPHPPFFEVYRNSESVTPNPRSPL
EDYSLHIIDLHTGRLCDTRTFKCDKVVLSHNQGLYLYKNILAILSVQQQTIHVFQVTPEG
TFIDVRTIGRFCYEDDLLTVSAVFPEVQRDSQTGMANPFRDPFINSLKHRLLVYLWRRAE
QDGSAMAKRRFFQYFDQLRQLRMWKMQLLDENHLFIKYTSEDVVTLRVTDPSQASFFVVY
NMVTTEVIAVFENTSDELLELFENFCDLFRNATLHSEVQFPCSASSNNFARQIQRRFKDT
IINAKYGGHTEAVRRLLGQLPISAQSYSGSPYLDLSLFSYDDKWVSVMERPKTCGDHPIR
FYARDSGLLKFEIQAGLLGRPINHTVRRLVAFTFHPFEPFAISVQRTNAEYVVNFHMRHC
CT

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)
9LTR 3.03 Å, Cryo-EM structure of dimeric DDB1-DDA1-DET1-Ube2e2-COP1 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
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)

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