9BJZ: Human DDD-Ube2e2 complex

Structure of the human DDD-Ube2e2 complex. Determined by electron microscopy at 2.83 Å resolution. Released 5 Mar 2025.

Method: Electron microscopy
Resolution: 2.83 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,999
Mol. weight: 199.45 kDa
Released: 5 Mar 2025

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

Secondary structure: helices and β-sheets

9BJZ contains 47 α-helices and 104 β-strands across 4 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: 13 helices, 72 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	1
β-strand	17-21	5	2
β-strand	30-35	6	2
β-strand	38-45	8	2
β-strand	48-56	9	2
β-strand	61-67	7	3
β-strand	76-81	6	3
β-strand	85-94	10	3
β-strand	97-107	11	3
α-helix	114	1
β-strand	115	1	4
α-helix	116	1
β-strand	121-124	4	5
β-strand	131-134	4	5
β-strand	136	1	4
β-strand	139	1	6
β-strand	141-142	2	5
β-strand	151-154	4	3
β-strand	155	1	5
β-strand	158	1	6
β-strand	163-169	7	7
β-strand	177-184	8	7
β-strand	187-196	10	7
β-strand	201-204	4	7
β-strand	210-212	3	7
β-strand	218-221	4	8
β-strand	229-232	4	8
β-strand	237-241	5	8
β-strand	244-248	5	8
α-helix	253-255	3
β-strand	258-263	6	9
β-strand	270-275	6	9
β-strand	279-289	11	9
β-strand	295-307	13	9
α-helix	310-311	2
β-strand	313-318	6	10
β-strand	321-325	5	10
β-strand	331-336	6	10
β-strand	347-353	7	10
β-strand	362-365	4	11
β-strand	374-379	6	11
α-helix	382-384	3
β-strand	386-391	6	11
β-strand	711-716	6	11
β-strand	720-727	8	12
β-strand	732-743	12	12
β-strand	749-751	3	12
β-strand	762-765	4	12
β-strand	785-795	11	12
β-strand	801-806	6	12
α-helix	807-808	2
β-strand	811-819	9	13
β-strand	828-835	8	13
β-strand	846-854	9	13
β-strand	857-862	6	13
β-strand	865-866	2	13
β-strand	870-876	7	14
β-strand	879-884	6	14
β-strand	887-893	7	14
β-strand	899-905	7	14
β-strand	911-917	7	15
β-strand	920-925	6	15
β-strand	930-936	7	15
β-strand	941-947	7	15
β-strand	954-959	6	16
β-strand	964-969	6	16
β-strand	973-979	7	16
α-helix	988-990	3
β-strand	991	1	15
β-strand	992-999	8	16
β-strand	1004-1009	6	1
β-strand	1024-1032	9	1
β-strand	1037-1043	7	1
α-helix	1045-1061	17
α-helix	1063-1064	2
α-helix	1070-1073	4
β-strand	1076-1077	2	17
β-strand	1082-1083	2	17
β-strand	1086	1	16
β-strand	1088-1090	3	1
α-helix	1091-1096	6
α-helix	1102-1109	8
β-strand	1113-1115	3	18
β-strand	1121-1123	3	18
α-helix	1126-1137	12

Chain B: 26 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
α-helix	18-27	10
α-helix	35-40	6
α-helix	41-44	4
β-strand	50-53	4	19
β-strand	61-65	5	20
β-strand	71-75	5	20
β-strand	81-87	7	20
α-helix	94-97	4
α-helix	111-124	14
β-strand	125-132	8	20
β-strand	139-140	2	21
β-strand	146-147	2	21
β-strand	153-161	9	21
α-helix	162-163	2
α-helix	167-169	3
α-helix	170-173	4
α-helix	179-183	5
β-strand	189-197	9	21
β-strand	203-212	10	21
α-helix	217-219	3
β-strand	222-225	4	22
β-strand	228-233	6	22
β-strand	238-244	7	22
β-strand	250-256	7	22
α-helix	264-271	8
α-helix	292-293	2
α-helix	294-310	17
α-helix	313-321	9
α-helix	323-327	5
β-strand	330-333	4	23
β-strand	336	1	23
β-strand	341-347	7	23
α-helix	349-352	4
α-helix	358-360	3
β-strand	364-369	6	23
β-strand	375-379	5	23
α-helix	384-392	9
α-helix	394-398	5
α-helix	416-430	15
α-helix	437-444	8
α-helix	448	1
α-helix	450-451	2
α-helix	459-461	3
β-strand	466-467	2	24
α-helix	486	1
β-strand	487-491	5	24
β-strand	497-501	5	24
β-strand	517-522	6	19
β-strand	528-535	8	19
β-strand	538-545	8	19

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	45-49	5	3
α-helix	54-68	15

Chain D: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	55-69	15
β-strand	75-80	6	25
β-strand	83-92	10	25
β-strand	103-109	7	25
α-helix	118-119	2
β-strand	120-123	4	25
β-strand	132	1	26
β-strand	138	1	26
α-helix	141-143	3
α-helix	153-165	13
α-helix	175-182	8
α-helix	185-195	11
α-helix	196-200	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A	protein	853	Homo sapiens	Q16531 (AlphaFold model)
DET1 homolog	B	protein	589	Homo sapiens	Q7L5Y6 (AlphaFold model)
DET1- and DDB1-associated protein 1	C	protein	102	Homo sapiens	Q9BW61 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 E2	D	protein	220	Homo sapiens	Q96LR5 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9BJZ_1 DNA damage-binding protein 1 (chains A)
MAHHHHHHSAALEVLFQMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYV
VTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITR
AHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELH
VIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVP
EPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFML
LLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQ
GSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGGNGNSGEI
QKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSS
SKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNT
YFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINST
VRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIAR
DFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVF
CHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGK
IEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATAD
DLIKVVEELTRIH

Sequence of entity 2 (B), FASTA

>9BJZ_2 DET1 homolog (chains B)
MSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKLEVLFQGPGDHHVSTIKPRRIQNQNVIHR
LERRRISSGKAGTHWHQVRVFHQNVFPNFTVVNVEKPPCFLRKFSPDGRYFIAFSSDQTS
LEIYEYQGCQAAEDLLQGYEGEILSNGNDQRSVNIRGRLFERFFVLLHITNVAANGEHLN
RECSLFTDDCRCVIVGSAAYLPDEPHPPFFEVYRNSESVTPNPRSPLEDYSLHIIDLHTG
RLCDTRTFKCDKVVLSHNQGLYLYKNILAILSVQQQTIHVFQVTPEGTFIDVRTIGRFCY
EDDLLTVSAVFPEVQRDSQTGMANPFRDPFINSLKHRLLVYLWRRAEQDGSAMAKRRFFQ
YFDQLRQLRMWKMQLLDENHLFIKYTSEDVVTLRVTDPSQASFFVVYNMVTTEVIAVFEN
TSDELLELFENFCDLFRNATLHSEVQFPCSASSNNFARQIQRRFKDTIINAKYGGHTEAV
RRLLGQLPISAQSYSGSPYLDLSLFSYDDKWVSVMERPKTCGDHPIRFYARDSGLLKFEI
QAGLLGRPINHTVRRLVAFTFHPFEPFAISVQRTNAEYVVNFHMRHCCT

Sequence of entity 3 (C), FASTA

>9BJZ_3 DET1- and DDB1-associated protein 1 (chains C)
MADFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLH
QQWDKKNAAKKRDQEQVELEGESSAPPRKVARTDSPDMHEDT

Sequence of entity 4 (D), FASTA

>9BJZ_4 Ubiquitin-conjugating enzyme E2 E2 (chains D)
MAHHHHHHSAALEVLFQGPGSTEAQRVDDSPSTSGGSSDGDQRESVQQEPEREQVQPKKK
EGKISSKTAAKLSTSAKRIQKELAEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEG
GVFFLDITFSPDYPFKPPKVTFRTRIYHCNINSQGVICLDILKDNWSPALTISKVLLSIC
SLLTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT

Primary citation

DET1 dynamics underlie cooperative ubiquitination by CRL4 DET1-COP1 complexes. Burgess, A.E., Loughran, T.A., Turk, L.S. et al. Sci Adv (2025) 11:eadq4187-eadq4187. DOI 10.1126/sciadv.adq4187 · PubMed

Other PDB entries of the same protein (UniProt Q16531 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BBG 1.7 Å, Co-crystal structure of human DDB1 bound to fragment UB028671
9EJQ 1.87 Å, Crystal structure of DDB1 in complex with XS381952
9BBI 1.9 Å, Co-crystal structure of human DDB1 bound to fragment UB028669
9BZ0 1.9 Å, Structure of an STK19-containing TC-NER complex
9BBE 2.0 Å, Co-crystal structure of human DDB1 bound to fragment UB028668
9BBH 2.0 Å, Co-crystal structure of human DDB1 bound to fragment UB028670
9FJX 2.0 Å, Crystal structure of human CRBN-DDB1 in complex with Lenalidomide
9ZXN 2.07 Å, DDB1 delta with compound 26
37MF 2.1 Å, Crystal structure of DDB1 in complex with XS445479
9ZXM 2.19 Å, DDB1 delta with compound 6
8G46 2.2 Å, Cryo-EM structure of DDB1deltaB-DDA1-DCAF16-BRD4(BD2)-MMH2
8ZSW 2.25 Å, Crystal Structure of Human DDB1, a Component of the E3 Ubiquitin Ligase Complex

Browse structure collections

About this viewer

MolViewer shows 9BJZ 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.