9M0Y: E3 ubiquitin-protein ligase COP1

Name: PDB 9M0Y: Local refinement of stacked like DDB1-DDA1-DET1-Ube2e2-COP1 complex (layer 2)
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 2). Determined by electron microscopy at 4.25 Å resolution. Released 28 Jan 2026.

Method: Electron microscopy
Resolution: 4.25 Å
Organism: Homo sapiens
Chains: 16
Atoms: 36,013
Mol. weight: 1094.89 kDa
Released: 28 Jan 2026

Explore 9M0Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9M0Y contains 153 α-helices and 480 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, 30 β-strands

Element	Residues	Length	Sheet
α-helix	219-228	10
α-helix	237-283	47
α-helix	348-362	15
α-helix	364-375	12
α-helix	382-398	17
β-strand	405-412	8	1
β-strand	422	1	2
β-strand	424-429	6	3
β-strand	435-440	6	3
β-strand	444-449	6	3
α-helix	450-455	6
β-strand	465-468	4	3
α-helix	472	1
β-strand	473-478	6	4
β-strand	485-490	6	4
β-strand	495-499	5	4
β-strand	505-509	5	4
β-strand	516-521	6	5
β-strand	528-533	6	5
β-strand	537-542	6	5
β-strand	548-553	6	5
β-strand	558-563	6	6
β-strand	571-575	5	6
β-strand	579-583	5	6
β-strand	591-596	6	6
β-strand	602-606	5	7
β-strand	612-617	6	7
β-strand	621-626	6	7
β-strand	632-636	5	7
β-strand	648-651	4	8
β-strand	654-659	6	8
β-strand	663-667	5	8
β-strand	674-678	5	8
β-strand	702-705	4	1
β-strand	715-719	5	1
β-strand	722	1	2
β-strand	724-730	7	1

Chain B: 7 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	9
β-strand	424-429	6	10
β-strand	435-440	6	10
β-strand	444-449	6	10
α-helix	450-455	6
β-strand	465-468	4	10
α-helix	472	1
β-strand	473-478	6	11
β-strand	485-490	6	11
β-strand	495-499	5	11
β-strand	504-509	6	11
β-strand	516-521	6	12
β-strand	528-533	6	12
β-strand	537-542	6	12
β-strand	548-553	6	12
β-strand	560-563	4	13
β-strand	570-574	5	13
β-strand	579-584	6	13
β-strand	593-596	4	13
β-strand	605-606	2	14
β-strand	612-617	6	14
β-strand	621-626	6	14
β-strand	632-637	6	14
β-strand	648-651	4	15
β-strand	654-659	6	15
β-strand	663-667	5	15
β-strand	674-678	5	15
β-strand	702-705	4	9
β-strand	715-719	5	9
β-strand	724-730	7	9

Chain C: 12 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	130-134	5
β-strand	135-136	2	16
β-strand	141-142	2	16
β-strand	147-148	2	17
β-strand	154-155	2	17
α-helix	157-166	10
β-strand	169-170	2	18
β-strand	175-176	2	18
α-helix	177	1
α-helix	180-182	3
β-strand	184-185	2	17
α-helix	187-202	16
α-helix	217-228	12
α-helix	235-301	67
α-helix	352-362	11
α-helix	364-375	12
α-helix	384-399	16
β-strand	405-412	8	19
β-strand	424-428	5	20
β-strand	435-440	6	20
β-strand	444-449	6	20
α-helix	450-455	6
β-strand	465-468	4	20
β-strand	473-478	6	21
β-strand	486-490	5	21
β-strand	495-498	4	21
β-strand	505-509	5	21
β-strand	516-521	6	22
β-strand	528-533	6	22
β-strand	537-542	6	22
β-strand	550-553	4	22
β-strand	558-563	6	23
β-strand	570-575	6	23
β-strand	579-584	6	23
β-strand	593-596	4	23
β-strand	602-606	5	24
β-strand	612-617	6	24
β-strand	621-626	6	24
β-strand	632-634	3	24
β-strand	648-651	4	25
β-strand	654-657	4	25
β-strand	664-668	5	25
β-strand	676-678	3	25
α-helix	680-682	3
β-strand	703-704	2	19
β-strand	715-719	5	19
β-strand	724-730	7	19

Chain D: 11 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	132-134	3
β-strand	135	1	26
β-strand	142	1	26
β-strand	146-148	3	27
β-strand	154-156	3	27
α-helix	157-166	10
α-helix	180-182	3
β-strand	185	1	27
α-helix	188-202	15
α-helix	237-248	12
α-helix	251-301	51
α-helix	347-362	16
α-helix	364-375	12
α-helix	384-399	16
β-strand	406-411	6	28
β-strand	426-428	3	29
β-strand	435-439	5	29
β-strand	444-449	6	29
α-helix	450-455	6
β-strand	465-468	4	29
β-strand	473-478	6	30
β-strand	485-490	6	30
β-strand	495-499	5	30
β-strand	505-509	5	30
β-strand	516-521	6	31
β-strand	528-533	6	31
β-strand	538-542	5	31
β-strand	548-552	5	31
β-strand	560-563	4	32
β-strand	570-574	5	32
β-strand	579-584	6	32
β-strand	587-596	10	32
β-strand	602-606	5	33
β-strand	612-617	6	33
β-strand	622-626	5	33
β-strand	632-636	5	33
β-strand	648-651	4	34
β-strand	654-657	4	34
β-strand	663-667	5	34
β-strand	676-679	4	34
α-helix	680-681	2
β-strand	700-704	5	28
β-strand	715-720	6	28
β-strand	725-729	5	28

Chain E: 10 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	132-134	3
β-strand	135-136	2	35
β-strand	141-142	2	35
β-strand	147-148	2	36
β-strand	154-155	2	36
α-helix	157-166	10
β-strand	169	1	37
β-strand	176	1	37
β-strand	184-185	2	36
α-helix	187-202	16
α-helix	217-228	12
α-helix	235-301	67
α-helix	352-362	11
α-helix	364-375	12
α-helix	384-399	16
β-strand	405-412	8	38
β-strand	424-429	6	39
β-strand	435-440	6	39
β-strand	444-449	6	39
α-helix	450-455	6
β-strand	465-468	4	39
α-helix	472	1
β-strand	473-478	6	40
β-strand	486-490	5	40
β-strand	495-498	4	40
β-strand	505-509	5	40
β-strand	516-521	6	41
β-strand	528-533	6	41
β-strand	537-542	6	41
β-strand	550-553	4	41
β-strand	558-562	5	42
β-strand	570-575	6	42
β-strand	579-584	6	42
β-strand	593-596	4	42
β-strand	602-606	5	43
β-strand	612-617	6	43
β-strand	621-626	6	43
β-strand	632-636	5	43
β-strand	648-651	4	44
β-strand	654-657	4	44
β-strand	664-668	5	44
β-strand	676-678	3	44
β-strand	700-704	5	38
β-strand	715-720	6	38
β-strand	724-730	7	38

Chain F: 10 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	130-134	5
β-strand	135	1	45
β-strand	142	1	45
β-strand	147-148	2	46
β-strand	154-155	2	46
α-helix	157-166	10
α-helix	175-177	3
α-helix	180-182	3
β-strand	184-185	2	46
α-helix	187-202	16
α-helix	235-301	67
α-helix	347-362	16
α-helix	364-375	12
α-helix	383-399	17
β-strand	405-410	6	47
β-strand	424-428	5	48
β-strand	435-440	6	48
β-strand	444-449	6	48
α-helix	450-455	6
β-strand	465-468	4	48
β-strand	473-478	6	49
β-strand	485-490	6	49
β-strand	495-499	5	49
β-strand	505-509	5	49
β-strand	516-521	6	50
β-strand	528-533	6	50
β-strand	538-542	5	50
β-strand	548-552	5	50
β-strand	558-563	6	51
β-strand	570-575	6	51
β-strand	579-584	6	51
β-strand	587-596	10	51
β-strand	602-606	5	52
β-strand	612-617	6	52
β-strand	622-626	5	52
β-strand	632-636	5	52
β-strand	648-651	4	53
β-strand	654-658	5	53
β-strand	663-667	5	53
β-strand	674-679	6	53
β-strand	700-704	5	47
β-strand	715-720	6	47
β-strand	725-730	6	47

Chain G: 5 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	235-301	67
α-helix	348-362	15
α-helix	364-375	12
α-helix	384-400	17
β-strand	405-412	8	54
β-strand	424-429	6	55
β-strand	435-440	6	55
β-strand	444-449	6	55
α-helix	450-455	6
β-strand	465-468	4	55
β-strand	473-478	6	56
β-strand	485-490	6	56
β-strand	494-499	6	56
β-strand	505-510	6	56
β-strand	516-521	6	57
β-strand	528-533	6	57
β-strand	537-542	6	57
β-strand	548-553	6	57
β-strand	558-563	6	58
β-strand	570	1	59
β-strand	571-575	5	58
β-strand	580-583	4	58
β-strand	584	1	59
β-strand	591-594	4	58
β-strand	602-606	5	60
β-strand	613-617	5	60
β-strand	622-625	4	60
β-strand	632-636	5	60
β-strand	648-651	4	61
β-strand	654-658	5	61
β-strand	664-668	5	61
β-strand	676-678	3	61
β-strand	702-705	4	54
β-strand	715-719	5	54
β-strand	724-730	7	54

Chain j: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	40-43	4
α-helix	54-64	11

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	A, B, C, D, E, F, G, J	protein	731	Homo sapiens	Q8NHY2 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 E2	Q, T	protein	201	Homo sapiens	Q96LR5 (AlphaFold model)
DET1 homolog	R, U	protein	550	Homo sapiens	Q7L5Y6 (AlphaFold model)
DNA damage-binding protein 1	S, V	protein	1140	Homo sapiens	Q16531 (AlphaFold model)
DET1- and DDB1-associated protein 1	j, n	protein	102	Homo sapiens	Q9BW61

Sequence of entity 1 (A, B, C, D, E, F, G, J), FASTA

>9M0Y_1 E3 ubiquitin-protein ligase COP1 (chains A, B, C, D, E, F, G, J)
MSGSRQAGSGSAGTSPGSSAASSVTSASSSLSSSPSPPSVAVSAAALVSGGVAQAAGSGG
LGGPVRPVLVAPAVSGSGGGAVSTGLSRHSCAARPSAGVGGSSSSLGSGSRKRPLLAPLC
NGLINSYEDKSNDFVCPICFDMIEEAYMTKCGHSFCYKCIHQSLEDNNRCPKCNYVVDNI
DHLYPNFLVNELILKQKQRFEEKRFKLDHSVSSTNGHRWQIFQDWLGTDQDNLDLANVNL
MLELLVQKKKQLEAESHAAQLQILMEFLKVARRNKREQLEQIQKELSVLEEDIKRVEEMS
GLYSPVSEDSTVPQFEAPSPSHSSIIDSTEYSQPPGFSGSSQTKKQPWYNSTLASRRKRL
TAHFEDLEQCYFSTRMSRISDDSRTASQLDEFQECLSKFTRYNSVRPLATLSYASDLYNG
SSIVSSIEFDRDCDYFAIAGVTKKIKVYEYDTVIQDAVDIHYPENEMTCNSKISCISWSS
YHKNLLASSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFNLMDPKLLASGSDDAKVKL
WSTNLDNSVASIEAKANVCCVKFSPSSRYHLAFGCADHCVHYYDLRNTKQPIMVFKGHRK
AVSYAKFVSGEEIVSASTDSQLKLWNVGKPYCLRSFKGHINEKNFVGLASNGDYIACGSE
NNSLYLYYKGLSKTLLTFKFDTVKSVLDKDRKEDDTNEFVSAVCWRALPDGESNVLIAAN
SQGTIKVLELV

Sequence of entity 2 (Q, T), FASTA

>9M0Y_2 Ubiquitin-conjugating enzyme E2 E2 (chains Q, T)
MSTEAQRVDDSPSTSGGSSDGDQRESVQQEPEREQVQPKKKEGKISSKTAAKLSTSAKRI
QKELAEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSPDYPFKPPK
VTFRTRIYHCNINSQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQ
YMTNRAEHDRMARQWTKRYAT

Sequence of entity 3 (R, U), FASTA

>9M0Y_3 DET1 homolog (chains R, U)
MDHHVSTIKPRRIQNQNVIHRLERRRISSGKAGTHWHQVRVFHQNVFPNFTVVNVEKPPC
FLRKFSPDGRYFIAFSSDQTSLEIYEYQGCQAAEDLLQGYEGEILSNGNDQRSVNIRGRL
FERFFVLLHITNVAANGEHLNRECSLFTDDCRCVIVGSAAYLPDEPHPPFFEVYRNSESV
TPNPRSPLEDYSLHIIDLHTGRLCDTRTFKCDKVVLSHNQGLYLYKNILAILSVQQQTIH
VFQVTPEGTFIDVRTIGRFCYEDDLLTVSAVFPEVQRDSQTGMANPFRDPFINSLKHRLL
VYLWRRAEQDGSAMAKRRFFQYFDQLRQLRMWKMQLLDENHLFIKYTSEDVVTLRVTDPS
QASFFVVYNMVTTEVIAVFENTSDELLELFENFCDLFRNATLHSEVQFPCSASSNNFARQ
IQRRFKDTIINAKYGGHTEAVRRLLGQLPISAQSYSGSPYLDLSLFSYDDKWVSVMERPK
TCGDHPIRFYARDSGLLKFEIQAGLLGRPINHTVRRLVAFTFHPFEPFAISVQRTNAEYV
VNFHMRHCCT

Sequence of entity 4 (S, V), FASTA

>9M0Y_4 DNA damage-binding protein 1 (chains S, V)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 5 (j, n), FASTA

>9M0Y_5 DET1- and DDB1-associated protein 1 (chains j, n)
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 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
9LUL 4.99 Å, Local refinement of stacked like DDB1-DDA1-DET1-Ube2e2-COP1 complex (layer 1)

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