6Q0R: DDB1-DDA1-DCAF15 complex

Structure of DDB1-DDA1-DCAF15 complex bound to E7820 and RBM39. Determined by X-ray diffraction at 2.9 Å resolution. Released 13 Nov 2019.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 5
Atoms: 10,249
Mol. weight: 185.03 kDa
Ligands: OXM, O6M, ZN
Released: 13 Nov 2019

Explore 6Q0R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Q0R contains 33 α-helices and 101 β-strands across 5 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, 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
β-strand	115	1	4
β-strand	121-124	4	4
β-strand	130-136	7	4
β-strand	139-144	6	4
β-strand	151-154	4	3
β-strand	155-158	4	4
β-strand	164-169	6	5
α-helix	170	1
β-strand	177-184	8	5
β-strand	187-196	10	5
β-strand	201-204	4	5
β-strand	210-212	3	5
β-strand	218-221	4	6
β-strand	229-232	4	6
β-strand	237-241	5	6
β-strand	244-248	5	6
α-helix	251-253	3
β-strand	258-263	6	7
β-strand	270-275	6	7
β-strand	279-289	11	7
β-strand	295-307	13	7
β-strand	311-316	6	8
β-strand	321-326	6	8
β-strand	331-336	6	8
β-strand	347-353	7	8
β-strand	361-363	3	9
β-strand	375-379	5	9
α-helix	382-384	3
β-strand	386-391	6	9
β-strand	711-716	6	9
β-strand	720-727	8	10
α-helix	728-730	3
β-strand	732-743	12	10
β-strand	749-751	3	10
α-helix	756-758	3
β-strand	762-765	4	10
β-strand	786-795	10	10
β-strand	801-806	6	10
α-helix	807-808	2
β-strand	811-819	9	11
β-strand	828-835	8	11
β-strand	846-854	9	11
β-strand	857-866	10	11
β-strand	870-876	7	12
β-strand	879-884	6	12
β-strand	887-893	7	12
β-strand	899-905	7	12
β-strand	911-917	7	13
β-strand	920-925	6	13
β-strand	930-936	7	13
β-strand	941-947	7	13
β-strand	954-961	8	14
β-strand	964-969	6	14
β-strand	973-979	7	14
α-helix	986-989	4
β-strand	991	1	13
β-strand	992-999	8	14
β-strand	1004-1008	5	1
β-strand	1025-1032	8	1
β-strand	1037-1042	6	1
α-helix	1045-1061	17
α-helix	1070-1074	5
β-strand	1076-1077	2	15
β-strand	1082-1083	2	15
β-strand	1086	1	14
β-strand	1088-1090	3	1
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1108	7
α-helix	1126-1137	12

Chain B: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	36-46	11
α-helix	51-54	4
α-helix	58-59	2
β-strand	61-64	4	16
α-helix	65-67	3
α-helix	71-73	3
β-strand	79-83	5	17
β-strand	89-96	8	17
β-strand	105	1	18
β-strand	106-113	8	17
α-helix	119-120	2
β-strand	121-128	8	17
β-strand	134	1	18
β-strand	139-144	6	19
β-strand	151-157	7	19
β-strand	162	1	20
β-strand	173	1	20
β-strand	179-186	8	19
α-helix	187-189	3
α-helix	194-197	4
β-strand	217-223	7	19
α-helix	228-231	4
α-helix	233-236	4
β-strand	242-246	5	21
β-strand	250-258	9	21

Chain C: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	387-394	8	21
β-strand	420	1	19
β-strand	430	1	21
β-strand	441-449	9	21
α-helix	450-461	12
α-helix	463-466	4
β-strand	468-482	15	22
β-strand	487-498	12	22
β-strand	511-522	12	22
β-strand	528-533	6	22
β-strand	537-538	2	22
α-helix	544-562	19
α-helix	565-567	3
α-helix	568-570	3
β-strand	573-575	3	19
β-strand	588-591	4	16
α-helix	592-594	3
β-strand	596-599	4	16

Chain D: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	250-255	6	23
α-helix	263-270	8
α-helix	271-273	3
β-strand	276-284	9	23
β-strand	289-298	10	23
α-helix	301-311	11
β-strand	315-316	2	24
β-strand	319-320	2	24
β-strand	322-325	4	23

Chain E: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	34	1	2
β-strand	45-49	5	3
α-helix	54-68	15

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 15	B	protein	276	Homo sapiens	Q66K64 (AlphaFold model)
DDB1- and CUL4-associated factor 15	C	protein	263	Homo sapiens	Q66K64 (AlphaFold model)
RNA-binding protein 39	D	protein	107	Homo sapiens	Q14498 (AlphaFold model)
DET1- and DDB1-associated protein 1	E	protein	126	Homo sapiens	Q9BW61 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6Q0R_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

>6Q0R_2 DDB1- and CUL4-associated factor 15 (chains B)
MDWSHPQFEKSAVGLNDIFEAQKIEWHEGGGGSGENLYFQGGGRMGRRREHVLKQLERVK
ISGQLSPRLFRKLPPRVCVSLKNIVDEDFLYAGHIFLGFSKCGRYVLSYTSSSGDDDFSF
YIYHLYWWEFNVHSKLKLVRQVRLFQDEEIYSDLYLTVCEWPSDASKVIVFGFNTRSANG
MLMNMMMMSDENHRDIYVSTVAVPPPGRCAACQDASRAHPGDPNAQCLRHGFMLHTKYQV
VYPFPTFQPAFQLKKDQVVLLNTSYSLVACAVSVHS

Sequence of entity 3 (C), FASTA

>6Q0R_3 DDB1- and CUL4-associated factor 15 (chains C)
MDWSHPQFEKSAVGLNDIFEAQKIEWHEGGGGSGENLYFQGGGRMEPGYVNYTKLYYVLE
SGEGTEPEDELEDDKISLPFVVTDLRGRNLRPMRERTAVQGQYLTVEQLTLDFEYVINEV
IRHDATWGHQFCSFSDYDIVILEVCPETNQVLINIGLLLLAFPSPTEEGQLRPKTYHTSL
KVAWDLNTGIFETVSVGDLTEVKGQTSGSVWSSYRKSCVDMVMKWLVPESSGRYVNRMTN
EALHKGCSLKVLADSERYTWIVL

Sequence of entity 4 (D), FASTA

>6Q0R_4 RNA-binding protein 39 (chains D)
MGSSHHHHHHSAVDENLYFQGGGRMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDS
ETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTDA

Sequence of entity 5 (E), FASTA

>6Q0R_5 DET1- and DDB1-associated protein 1 (chains E)
MGSSHHHHHHSAVDENLYFQGGGRMADFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYL
PTREYPSEQIIVTEKTNILLRYLHQQWDKKNAAKKRDQEQVELEGESSAPPRKVARTDSP
DMHEDT

Ligands and cofactors

ID	Name	Formula	Copies
OXM	Oxamic acid	C2 H3 N O3	1
O6M	3-cyano-N-(3-cyano-4-methyl-1H-indol-7-yl)benzene-1-sulfonamide	C17 H12 N4 O2 S	1
ZN	Zinc ion	Zn	1

Primary citation

Structural complementarity facilitates E7820-mediated degradation of RBM39 by DCAF15. Faust, T.B., Yoon, H., Nowak, R.P. et al. Nat Chem Biol (2020) 16:7-14. DOI 10.1038/s41589-019-0378-3 · 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

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