9LU1: Protein structure of DDB1-DDA1-DET1-Ube2e2

Name: PDB 9LU1: protein structure of DDB1-DDA1-DET1-Ube2e2 bound to COP1 dimer
Published: 2026-01-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

protein structure of DDB1-DDA1-DET1-Ube2e2 bound to COP1 dimer. Determined by electron microscopy at 3.62 Å resolution. Released 28 Jan 2026.

Method: Electron microscopy
Resolution: 3.62 Å
Organism: Homo sapiens
Chains: 6
Atoms: 17,116
Mol. weight: 386.26 kDa
Released: 28 Jan 2026

Explore 9LU1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9LU1 contains 47 α-helices and 198 β-strands across 6 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, 29 β-strands

Element	Residues	Length	Sheet
α-helix	258-300	43
α-helix	353-362	10
α-helix	364-372	9
α-helix	389-399	11
β-strand	406-412	7	1
β-strand	424-428	5	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	486-490	5	3
β-strand	495-498	4	3
β-strand	518	1	4
β-strand	521	1	4
β-strand	529	1	4
β-strand	532	1	4
β-strand	537-541	5	4
β-strand	548-553	6	4
β-strand	561-563	3	5
β-strand	571-573	3	5
β-strand	580-583	4	6
β-strand	591-595	5	6
β-strand	602-607	6	7
β-strand	612-617	6	7
β-strand	622-626	5	7
β-strand	632-636	5	7
β-strand	648-650	3	8
β-strand	654-657	4	8
β-strand	665-668	4	8
β-strand	676	1	8
β-strand	700-705	6	1
β-strand	716-720	5	1
β-strand	724-729	6	1

Chain B: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	9
β-strand	47-49	3	10
α-helix	55-58	4
α-helix	61-65	5

Chain C: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	55-69	15
α-helix	71-72	2
β-strand	79	1	11
β-strand	87	1	11
β-strand	90-92	3	12
α-helix	93-94	2
β-strand	103-105	3	12
β-strand	106-109	4	11
α-helix	118-119	2
β-strand	120-123	4	11
β-strand	132	1	13
β-strand	138	1	13
α-helix	153-165	13
α-helix	175-183	9
α-helix	186-196	11

Chain E: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	262-300	39
α-helix	358-370	13
α-helix	390-401	12
β-strand	409-412	4	14
β-strand	424-428	5	15
β-strand	437-440	4	15
β-strand	445-447	3	15
α-helix	450-454	5
β-strand	465	1	15
β-strand	476-478	3	16
β-strand	486-488	3	16
β-strand	494-499	6	16
β-strand	504-510	7	16
β-strand	516-521	6	17
β-strand	528-533	6	17
β-strand	537-542	6	17
β-strand	550-553	4	17
β-strand	558-563	6	18
β-strand	570-575	6	18
β-strand	579-584	6	18
β-strand	593-596	4	18
α-helix	601	1
β-strand	602-609	8	19
β-strand	612-617	6	19
β-strand	623	1	19
β-strand	624	1	20
β-strand	634	1	20
β-strand	648	1	21
β-strand	654-659	6	21
β-strand	663-668	6	21
β-strand	700-703	4	14
β-strand	717-720	4	14
β-strand	724-727	4	14

Chain R: 16 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	18-27	10
α-helix	35-40	6
α-helix	41-45	5
β-strand	50-53	4	22
β-strand	61-65	5	23
β-strand	71-75	5	23
β-strand	81-87	7	23
α-helix	111-124	14
β-strand	125-132	8	23
β-strand	139-140	2	24
β-strand	146	1	24
β-strand	153-161	9	24
α-helix	167-169	3
α-helix	170-173	4
α-helix	179-183	5
β-strand	189-197	9	24
β-strand	203-212	10	24
α-helix	217-219	3
β-strand	222-225	4	25
β-strand	228-233	6	25
β-strand	238-244	7	25
β-strand	250-256	7	25
α-helix	265-268	4
α-helix	294-308	15
α-helix	316-320	5
β-strand	330-338	9	26
β-strand	341-347	7	26
α-helix	349-352	4
β-strand	364-369	6	26
β-strand	374-380	7	26
α-helix	385-392	8
α-helix	394-398	5
α-helix	418-430	13
α-helix	437-445	9
β-strand	455	1	27
β-strand	466-467	2	28
β-strand	476	1	27
β-strand	480-481	2	22
β-strand	487-491	5	28
β-strand	497-501	5	28
β-strand	517-522	6	22
β-strand	528-534	7	22
β-strand	539-545	7	22

Chain S: 12 helices, 104 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	29
β-strand	17-21	5	9
β-strand	30-35	6	9
β-strand	38-44	7	9
β-strand	49-56	8	9
β-strand	63-65	3	30
β-strand	77-80	4	30
β-strand	85-94	10	30
β-strand	97-107	11	30
α-helix	114	1
β-strand	115	1	31
α-helix	116	1
β-strand	121-124	4	32
β-strand	130-134	5	32
β-strand	136	1	31
β-strand	139-144	6	32
β-strand	152-154	3	10
β-strand	155-158	4	32
β-strand	164-169	6	33
β-strand	177-182	6	33
β-strand	189-196	8	33
β-strand	201-208	8	33
β-strand	216-222	7	34
β-strand	228-233	6	34
β-strand	237-241	5	34
β-strand	244-248	5	34
β-strand	258-263	6	35
β-strand	270-275	6	35
β-strand	279-286	8	35
β-strand	299-307	9	35
β-strand	311	1	36
β-strand	315-316	2	37
β-strand	321-324	4	37
β-strand	326	1	36
β-strand	331-336	6	37
β-strand	347-353	7	37
β-strand	359-364	6	38
β-strand	375-379	5	38
α-helix	382-384	3
β-strand	386-393	8	38
β-strand	394	1	39
β-strand	396-402	7	40
β-strand	411-413	3	41
β-strand	424-426	3	41
β-strand	435-437	3	41
β-strand	444-446	3	41
β-strand	457-460	4	42
β-strand	463	1	43
β-strand	467-468	2	43
β-strand	470-472	3	42
β-strand	476	1	42
β-strand	479-480	2	43
β-strand	486	1	43
β-strand	498-500	3	44
β-strand	503	1	44
β-strand	507-512	6	44
β-strand	515-522	8	44
β-strand	525-533	9	44
β-strand	538-542	5	45
β-strand	555	1	46
β-strand	557-560	4	45
β-strand	568-569	2	47
β-strand	570	1	46
β-strand	576-578	3	47
α-helix	586-588	3
β-strand	590-595	6	48
β-strand	600-605	6	48
β-strand	610-615	6	48
β-strand	627-630	4	48
β-strand	637-642	6	49
β-strand	647-652	6	49
β-strand	657-662	6	49
β-strand	665-670	6	49
β-strand	671	1	39
β-strand	676-680	5	40
β-strand	691-695	5	40
β-strand	699-704	6	40
β-strand	709-716	8	38
β-strand	720-727	8	50
β-strand	732-742	11	50
β-strand	764-765	2	51
β-strand	785-795	11	50
β-strand	801-804	4	50
β-strand	805-806	2	51
β-strand	812-817	6	52
β-strand	829-834	6	52
β-strand	846-854	9	52
β-strand	857-866	10	52
β-strand	870-876	7	53
β-strand	879-884	6	53
β-strand	888-893	6	53
β-strand	899-905	7	53
β-strand	913-917	5	54
β-strand	920-924	5	54
β-strand	930-935	6	54
β-strand	942-947	6	54
β-strand	954-959	6	55
β-strand	965-969	5	55
β-strand	973-979	7	55
α-helix	987-989	3
β-strand	991	1	54
β-strand	992-999	8	55
β-strand	1004-1009	6	29
β-strand	1025-1032	8	29
β-strand	1037-1042	6	29
α-helix	1045-1059	15
α-helix	1063-1064	2
α-helix	1070-1073	4
β-strand	1075	1	56
β-strand	1078	1	57
β-strand	1081	1	57
β-strand	1084	1	56
α-helix	1092-1095	4
α-helix	1096-1099	4
α-helix	1102-1108	7
α-helix	1126-1136	11

Molecules and chains

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

Sequence of entity 1 (A, E), FASTA

>9LU1_1 E3 ubiquitin-protein ligase COP1 (chains A, E)
MSGSRQAGSGSAGTSPGSSAASSVTSASSSLSSSPSPPSVAVSAAALVSGGVAQAAGSGG
LGGPVRPVLVAPAVSGSGGGAVSTGLSRHSCAARPSAGVGGSSSSLGSGSRKRPLLAPLC
NGLINSYEDKSNDFVCPICFDMIEEAYMTKCGHSFCYKCIHQSLEDNNRCPKCNYVVDNI
DHLYPNFLVNELILKQKQRFEEKRFKLDHSVSSTNGHRWQIFQDWLGTDQDNLDLANVNL
MLELLVQKKKQLEAESHAAQLQILMEFLKVARRNKREQLEQIQKELSVLEEDIKRVEEMS
GLYSPVSEDSTVPQFEAPSPSHSSIIDSTEYSQPPGFSGSSQTKKQPWYNSTLASRRKRL
TAHFEDLEQCYFSTRMSRISDDSRTASQLDEFQECLSKFTRYNSVRPLATLSYASDLYNG
SSIVSSIEFDRDCDYFAIAGVTKKIKVYEYDTVIQDAVDIHYPENEMTCNSKISCISWSS
YHKNLLASSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFNLMDPKLLASGSDDAKVKL
WSTNLDNSVASIEAKANVCCVKFSPSSRYHLAFGCADHCVHYYDLRNTKQPIMVFKGHRK
AVSYAKFVSGEEIVSASTDSQLKLWNVGKPYCLRSFKGHINEKNFVGLASNGDYIACGSE
NNSLYLYYKGLSKTLLTFKFDTVKSVLDKDRKEDDTNEFVSAVCWRALPDGESNVLIAAN
SQGTIKVLELV

Sequence of entity 2 (B), FASTA

>9LU1_2 DET1- and DDB1-associated protein 1 (chains B)
MADFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLH
QQWDKKNAAKKRDQEQVELEGESSAPPRKVARTDSPDMHEDT

Sequence of entity 3 (C), FASTA

>9LU1_3 Ubiquitin-conjugating enzyme E2 E2 (chains C)
MSTEAQRVDDSPSTSGGSSDGDQRESVQQEPEREQVQPKKKEGKISSKTAAKLSTSAKRI
QKELAEITLDPPPNCGAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSPDYPFKPPK
VTFRTRIYHCNINSQGVISLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQ
YMTNRAEHDRMARQWTKRYAT

Sequence of entity 4 (R), FASTA

>9LU1_4 DET1 homolog (chains R)
MDHHVSTIKPRRIQNQNVIHRLERRRISSGKAGTHWHQVRVFHQNVFPNFTVVNVEKPPC
FLRKFSPDGRYFIAFSSDQTSLEIYEYQGCQAAEDLLQGYEGEILSNGNDQRSVNIRGRL
FERFFVLLHITNVAANGEHLNRECSLFTDDCRCVIVGSAAYLPDEPHPPFFEVYRNSESV
TPNPRSPLEDYSLHIIDLHTGRLCDTRTFKCDKVVLSHNQGLYLYKNILAILSVQQQTIH
VFQVTPEGTFIDVRTIGRFCYEDDLLTVSAVFPEVQRDSQTGMANPFRDPFINSLKHRLL
VYLWRRAEQDGSAMAKRRFFQYFDQLRQLRMWKMQLLDENHLFIKYTSEDVVTLRVTDPS
QASFFVVYNMVTTEVIAVFENTSDELLELFENFCDLFRNATLHSEVQFPCSASSNNFARQ
IQRRFKDTIINAKYGGHTEAVRRLLGQLPISAQSYSGSPYLDLSLFSYDDKWVSVMERPK
TCGDHPIRFYARDSGLLKFEIQAGLLGRPINHTVRRLVAFTFHPFEPFAISVQRTNAEYV
VNFHMRHCCT

Sequence of entity 5 (S), FASTA

>9LU1_5 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

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
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)

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