8G46: DDB1deltaB-DDA1-DCAF16-BRD4(BD2)-MMH2

Cryo-EM structure of DDB1deltaB-DDA1-DCAF16-BRD4(BD2)-MMH2. Determined by electron microscopy at 2.2 Å resolution. Released 8 Mar 2023.

Method: Electron microscopy
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,603
Mol. weight: 148.65 kDa
Ligands: YK3, ZN
Released: 8 Mar 2023

Explore 8G46 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8G46 contains 33 α-helices and 69 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: 14 helices, 67 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	85-93	9	3
β-strand	98-107	10	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	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	210-211	2	5
β-strand	218-221	4	6
α-helix	222-223	2
β-strand	229-232	4	6
β-strand	237-240	4	6
β-strand	245-248	4	6
α-helix	251-255	5
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	313-318	6	8
β-strand	321-325	5	8
β-strand	331-336	6	8
β-strand	347-353	7	8
β-strand	361-365	5	9
β-strand	374-379	6	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	732-741	10	10
β-strand	751	1	10
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	811-820	10	11
β-strand	827-835	9	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	928	1	14
β-strand	930-936	7	13
β-strand	941-947	7	13
β-strand	952	1	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	13
β-strand	992-999	8	15
β-strand	1004-1009	6	1
β-strand	1025-1032	8	1
β-strand	1037-1042	6	1
α-helix	1045-1061	17
α-helix	1063-1064	2
α-helix	1070-1074	5
β-strand	1076-1077	2	16
β-strand	1082-1083	2	16
β-strand	1086	1	15
β-strand	1088-1090	3	1
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1109	8
α-helix	1126-1137	12

Chain B: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	48-60	13
β-strand	66-67	2	17
α-helix	68-70	3
α-helix	74-77	4
α-helix	88-94	7
β-strand	99-100	2	17
α-helix	107-111	5
α-helix	116-119	4
α-helix	131-138	8
α-helix	143-157	15
α-helix	161-163	3
α-helix	179-186	8
α-helix	201-215	15

Chain C: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	354-365	12
α-helix	370-373	4
α-helix	374-377	4
α-helix	390-393	4
α-helix	400-408	9
α-helix	415-432	18
α-helix	438-454	17

Chain E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3

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 16	B	protein	220	Homo sapiens	Q9NXF7 (AlphaFold model)
Bromodomain-containing protein 4	C	protein	129	Homo sapiens	O60885 (AlphaFold model)
DET1- and DDB1-associated protein 1	E	protein	106	Homo sapiens	Q9BW61 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8G46_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

>8G46_2 DDB1- and CUL4-associated factor 16 (chains B)
GGGRMGPRNPSPDHLSESESEEEENISYLNESSGEEWDSSEEEDSMVPNLSPLESLAWQV
KCLLKYSTTWKPLNPNSWLYHAKLLDPSTPVHILREIGLRLSHCSHCVPKLEPIPEWPPL
ASCGVPPFQKPLTSPSRLSRDHATLNGALQFATKQLSRTLSRATPIPEYLKQIPNSCVSG
CCCGWLTKTVKETTRTEPINTTYSYTDFQKAVNKLLTASL

Sequence of entity 3 (C), FASTA

>8G46_3 Bromodomain-containing protein 4 (chains C)
GKDVPDSQQHPAPEKSSKVSEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYC
DIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFE
MRFAKMPDE

Sequence of entity 4 (E), FASTA

>8G46_4 DET1- and DDB1-associated protein 1 (chains E)
GGGRMADFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILL
RYLHQQWDKKNAAKKRDQEQVELEGESSAPPRKVARTDSPDMHEDT

Ligands and cofactors

ID	Name	Formula	Copies
YK3	tert-butyl [(6S,10P)-4-{4-[(ethanesulfonyl)amino]phenyl}-2,3,9-trimethyl-6H-thi…	C25 H31 N5 O4 S2	1
ZN	Zinc ion	Zn	1

Primary citation

Template-assisted covalent modification of DCAF16 underlies activity of BRD4 molecular glue degraders. Li, Y.D., Ma, M.W., Hassan, M.M. et al. bioRxiv (2023). DOI 10.1101/2023.02.14.528208 · 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
8ZSW 2.25 Å, Crystal Structure of Human DDB1, a Component of the E3 Ubiquitin Ligase Complex
3EI3 2.3 Å, Structure of the hsDDB1-drDDB2 complex

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