8TL6: DDB1deltaB-DDA1-DCAF5

Cryo-EM structure of DDB1deltaB-DDA1-DCAF5. Determined by electron microscopy at 2.63 Å resolution. Released 3 Apr 2024.

Method: Electron microscopy
Resolution: 2.63 Å
Organism: Homo sapiens
Chains: 3
Atoms: 9,320
Mol. weight: 219.92 kDa
Released: 3 Apr 2024

Explore 8TL6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8TL6 contains 21 α-helices and 97 β-strands across 3 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: 14 helices, 66 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	130-134	5	5
β-strand	136	1	4
β-strand	139-144	6	5
β-strand	151-154	4	3
β-strand	155-158	4	5
β-strand	164-169	6	6
α-helix	170	1
β-strand	177-184	8	6
β-strand	187-196	10	6
β-strand	201-204	4	6
β-strand	210-211	2	6
β-strand	218-221	4	7
β-strand	229-232	4	7
β-strand	237-240	4	7
β-strand	245-248	4	7
α-helix	251-255	5
β-strand	258-263	6	8
β-strand	270-275	6	8
β-strand	279-289	11	8
β-strand	295-307	13	8
β-strand	313-318	6	9
β-strand	321-325	5	9
β-strand	331-336	6	9
β-strand	347-353	7	9
β-strand	361-365	5	10
β-strand	374-379	6	10
α-helix	382-384	3
β-strand	386-391	6	10
β-strand	711-716	6	10
β-strand	720-727	8	11
β-strand	732-742	11	11
α-helix	756-758	3
β-strand	762-765	4	11
β-strand	785-795	11	11
β-strand	801-806	6	11
α-helix	807-808	2
β-strand	811-819	9	12
β-strand	828-835	8	12
β-strand	846-854	9	12
β-strand	857-866	10	12
β-strand	870-876	7	13
β-strand	879-884	6	13
β-strand	887-893	7	13
β-strand	899-905	7	13
β-strand	911-917	7	14
β-strand	920-925	6	14
β-strand	930-936	7	14
β-strand	941-947	7	14
β-strand	954-959	6	15
β-strand	964-969	6	15
β-strand	973-979	7	15
α-helix	986-989	4
β-strand	991	1	14
β-strand	992-999	8	15
β-strand	1004-1009	6	1
β-strand	1024-1032	9	1
β-strand	1037-1043	7	1
α-helix	1045-1059	15
α-helix	1070-1074	5
β-strand	1076-1077	2	16
β-strand	1082-1083	2	16
β-strand	1086	1	15
β-strand	1089-1090	2	1
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1108	7
α-helix	1126-1137	12

Chain B: 6 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	14-24	11
α-helix	29-39	11
β-strand	45-49	5	17
β-strand	56-61	6	18
α-helix	62	1
β-strand	68-73	6	18
β-strand	78-82	5	18
α-helix	83-87	5
β-strand	94-95	2	18
β-strand	106-109	4	19
β-strand	116-119	4	19
β-strand	124-129	6	19
β-strand	134-140	7	19
β-strand	145-150	6	20
β-strand	157-162	6	20
β-strand	166-171	6	20
α-helix	172-174	3
β-strand	181-185	5	20
α-helix	189	1
β-strand	190-195	6	21
β-strand	202-207	6	21
β-strand	211-216	6	21
β-strand	223-227	5	21
β-strand	238-241	4	22
β-strand	247-251	5	22
β-strand	258-261	4	22
β-strand	267-272	6	22
β-strand	285-288	4	23
β-strand	294-298	5	23
β-strand	304-308	5	23
β-strand	321-323	3	22
β-strand	327-329	3	23
β-strand	336-342	7	17
β-strand	347-352	6	17
β-strand	357-361	5	17
β-strand	369	1	17

Chain E: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	45-49	5	3
α-helix	54-65	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A	protein	864	Homo sapiens	Q16531 (AlphaFold model)
DDB1- and CUL4-associated factor 5	B	protein	986	Homo sapiens	Q96JK2 (AlphaFold model)
DET1- and DDB1-associated protein 1	E	protein	126	Homo sapiens	Q9BW61 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8TL6_1 DNA damage-binding protein 1 (chains A)
MGSSHHHHHHSAAHIVMVDAYKPTKGGRMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLL
IAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYK
QSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKEL
KAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENV
EAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYL
LGDMEGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQ
LVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRN
GIGGNGNSGEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSA
STQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSL
VSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEF
NGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYK
PMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVG
LFHLGEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQN
RLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDD
GSGMKREATADDLIKVVEELTRIH

Sequence of entity 2 (B), FASTA

>8TL6_2 DDB1- and CUL4-associated factor 5 (chains B)
MDWSHPQFEKSAVGLNDIFEAQKIEWHEGGGGSGENLYFQGGGRMKRRAGLGGSMRSVVG
FLSQRGLHGDPLLTQDFQRRRLRGCRNLYKKDLLGHFGCVNAIEFSNNGGQWLVSGGDDR
RVLLWHMEQAIHSRVKPIQLKGEHHSNIFCLAFNSGNTKVFSGGNDEQVILHDVESSETL
DVFAHEDAVYGLSVSPVNDNIFASSSDDGRVLIWDIRESPHGEPFCLANYPSAFHSVMFN
PVEPRLLATANSKEGVGLWDIRKPQSSLLRYGGNLSLQSAMSVRFNSNGTQLLALRRRLP
PVLYDIHSRLPVFQFDNQGYFNSCTMKSCCFAGDRDQYILSGSDDFNLYMWRIPADPEAG
GIGRVVNGAFMVLKGHRSIVNQVRFNPHTYMICSSGVEKIIKIWSPYKQPGCTGDLDGRI
EDDSRCLYTHEEYISLVLNSGSGLSHDYANQSVQEDPRMMAFFDSLVRREIEGWSSDSDS
DLSESTILQLHAGVSERSGYTDSESSASLPRSPPPTVDESADNAFHLGPLRVTTTNTVAS
TPPTPTCEDAASRQQRLSALRRYQDKRLLALSNESDSEENVCEVELDTDLFPRPRSPSPE
DESSSSSSSSSSEDEEELNERRASTWQRNAMRRRQKTTREDKPSAPIKPTNTYIGEDNYD
YPQIKVDDLSSSPTSSPERSTSTLEIQPSRASPTSDIESVERKIYKAYKWLRYSYISYSN
NKDGETSLVTGEADEGRAGTSHKDNPAPSSSKEACLNIAMAQRNQDLPPEGCSKDTFKEE
TPRTPSNGPGHEHSSHAWAEVPEGTSQDTGNSGSVEHPFETKKLNGKALSSRAEEPPSPP
VPKASGSTLNSGSGNCPRTQSDDSEERSLETICANHNNGRLHPRPPHPHNNGQNLGELEV
VAYSSPGHSDTDRDNSSLTGTLLHKDCCGSEMACETPNAGTREDPTDTPATDSSRAVHGH
SGLKRQRIELEDTDSENSSSEKKLKT

Sequence of entity 3 (E), FASTA

>8TL6_3 DET1- and DDB1-associated protein 1 (chains E)
MGSSHHHHHHSAVDENLYFQGGGRMADFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYL
PTREYPSEQIIVTEKTNILLRYLHQQWDKKNAAKKRDQEQVELEGESSAPPRKVARTDSP
DMHEDT

Primary citation

Targeting DCAF5 suppresses SMARCB1-mutant cancer by stabilizing SWI/SNF. Radko-Juettner, S., Yue, H., Myers, J.A. et al. Nature (2024) 628:442-449. DOI 10.1038/s41586-024-07250-1 · 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

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