6UD7: DDB1- and CUL4-associated factor 15

Name: PDB 6UD7: Crystal structure of full-length human DCAF15-DDB1(deltaBPB)-DDA1-RBM39 in complex with indisulam
Published: 2019-12-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of full-length human DCAF15-DDB1(deltaBPB)-DDA1-RBM39 in complex with indisulam. Determined by X-ray diffraction at 2.3 Å resolution. Released 18 Dec 2019.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,635
Mol. weight: 181.29 kDa
Ligands: EF6
Released: 18 Dec 2019

Explore 6UD7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6UD7 contains 29 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: 11 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	33-35	3
α-helix	36-46	11
α-helix	58-59	2
β-strand	61-64	4	1
α-helix	65-68	4
β-strand	79-83	5	2
β-strand	89-96	8	2
β-strand	105	1	3
β-strand	106-113	8	2
α-helix	119-120	2
β-strand	121-128	8	2
β-strand	134	1	3
β-strand	139-144	6	4
β-strand	151-157	7	4
β-strand	161-162	2	5
β-strand	167	1	6
β-strand	170	1	6
β-strand	173-174	2	5
β-strand	178-186	9	4
α-helix	187-189	3
β-strand	217-224	8	4
α-helix	233-236	4
β-strand	242-246	5	7
β-strand	250-259	10	7
β-strand	389-395	7	7
β-strand	420-423	4	4
β-strand	430-432	3	7
β-strand	440-449	10	7
α-helix	450-460	11
β-strand	468-482	15	8
β-strand	487-498	12	8
α-helix	509-510	2
β-strand	511-522	12	8
β-strand	528-533	6	8
α-helix	534-536	3
β-strand	537-538	2	8
α-helix	544-561	18
β-strand	573-575	3	4
β-strand	588-591	4	1
β-strand	596-599	4	1

Chain B: 14 helices, 67 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	9
β-strand	17-21	5	10
β-strand	30-35	6	10
β-strand	38-44	7	10
β-strand	49-56	8	10
β-strand	61-67	7	11
β-strand	76-81	6	11
β-strand	85-94	10	11
β-strand	97-107	11	11
α-helix	114	1
β-strand	115	1	12
α-helix	116	1
β-strand	121-124	4	13
β-strand	130-134	5	13
β-strand	136	1	12
β-strand	139-144	6	13
β-strand	151-154	4	11
β-strand	155-158	4	13
β-strand	164-169	6	14
α-helix	170	1
β-strand	177-184	8	14
β-strand	187-196	10	14
β-strand	201-204	4	14
β-strand	210-211	2	14
β-strand	218-221	4	15
β-strand	229-232	4	15
β-strand	237-241	5	15
β-strand	244-248	5	15
α-helix	253-255	3
β-strand	258-263	6	16
β-strand	270-275	6	16
β-strand	279-289	11	16
β-strand	295-307	13	16
β-strand	313-318	6	17
β-strand	321-325	5	17
β-strand	331-336	6	17
β-strand	347-353	7	17
β-strand	359-365	7	18
β-strand	374-379	6	18
α-helix	382-384	3
β-strand	386-392	7	18
β-strand	710-716	7	18
β-strand	720-727	8	19
β-strand	732-743	12	19
β-strand	749-751	3	19
β-strand	762-765	4	19
β-strand	785-795	11	19
β-strand	801-806	6	19
α-helix	807-808	2
β-strand	811-820	10	20
β-strand	827-835	9	20
β-strand	846-853	8	20
β-strand	858-866	9	20
β-strand	870-876	7	21
β-strand	879-884	6	21
β-strand	887-893	7	21
β-strand	899-905	7	21
β-strand	911-917	7	22
β-strand	920-925	6	22
β-strand	930-936	7	22
β-strand	941-947	7	22
β-strand	954-961	8	23
β-strand	964-969	6	23
β-strand	973-979	7	23
α-helix	988-990	3
β-strand	991	1	22
β-strand	992-999	8	23
β-strand	1004-1009	6	9
β-strand	1024-1032	9	9
β-strand	1037-1043	7	9
α-helix	1045-1061	17
α-helix	1070-1074	5
β-strand	1076-1077	2	24
β-strand	1082-1083	2	24
β-strand	1086	1	23
β-strand	1088-1090	3	9
α-helix	1091-1095	5
α-helix	1096-1098	3
α-helix	1102-1104	3
α-helix	1129-1131	3
α-helix	1134-1137	4

Chain C: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	250-255	6	25
α-helix	263-270	8
α-helix	271-273	3
β-strand	276-283	8	25
β-strand	290-298	9	25
α-helix	301-311	11
β-strand	315-316	2	26
β-strand	319-320	2	26
β-strand	322-325	4	25

Chain D: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	33-34	2	10
β-strand	45-49	5	11
α-helix	54-68	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DDB1- and CUL4-associated factor 15	A	protein	601	Homo sapiens	Q66K64 (AlphaFold model)
DNA damage-binding protein 1,DNA damage-binding protein 1	B	protein	836	Homo sapiens	Q16531 (AlphaFold model)
RNA-binding motif protein 39	C	protein	81	Homo sapiens	Q14498 (AlphaFold model)
DET1- and DDB1-associated protein 1	D	protein	101	Homo sapiens	Q9BW61 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6UD7_1 DDB1- and CUL4-associated factor 15 (chains A)
GPAPSSKSERNSGAGSGGGGPGGAGGKRAAGRRREHVLKQLERVKISGQLSPRLFRKLPP
RVCVSLKNIVDEDFLYAGHIFLGFSKCGRYVLSYTSSSGDDDFSFYIYHLYWWEFNVHSK
LKLVRQVRLFQDEEIYSDLYLTVCEWPSDASKVIVFGFNTRSANGMLMNMMMMSDENHRD
IYVSTVAVPPPGRCAACQDASRAHPGDPNAQCLRHGFMLHTKYQVVYPFPTFQPAFQLKK
DQVVLLNTSYSLVACAVSVHSAGDRSFCQILYDHSTCPLAPASPPEPQSPELPPALPSFC
PEAAPARSSGSPEPSPAIAKAKEFVADIFRRAKEAKGGVPEEARPALCPGPSGSRCRAHS
EPLALCGETAPRDSPPASEAPASEPGYVNYTKLYYVLESGEGTEPEDELEDDKISLPFVV
TDLRGRNLRPMRERTAVQGQYLTVEQLTLDFEYVINEVIRHDATWGHQFCSFSDYDIVIL
EVCPETNQVLINIGLLLLAFPSPTEEGQLRPKTYHTSLKVAWDLNTGIFETVSVGDLTEV
KGQTSGSVWSSYRKSCVDMVMKWLVPESSGRYVNRMTNEALHKGCSLKVLADSERYTWIV
L

Sequence of entity 2 (B), FASTA

>6UD7_2 DNA damage-binding protein 1,DNA damage-binding protein 1 (chains B)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGGNGNSGEIQKLHIRTVPLYESPRKI
CYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGE
EVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPK
QGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECN
HYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDN
FLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPT
QGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEP
ATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 3 (C), FASTA

>6UD7_3 RNA-binding motif protein 39 (chains C)
GPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKA
LEQLNGFELAGRPMKVGHVTE

Sequence of entity 4 (D), FASTA

>6UD7_4 DET1- and DDB1-associated protein 1 (chains D)
ADFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLHQ
QWDKKNAAKKRDQEQVELEGESSAPPRKVARTDSPDMHEDT

Ligands and cofactors

ID	Name	Formula	Copies
EF6	N~1~-(3-chloro-1H-indol-7-yl)benzene-1,4-disulfonamide	C14 H12 Cl N3 O4 S2	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Structural basis of indisulam-mediated RBM39 recruitment to DCAF15 E3 ligase complex. Bussiere, D.E., Xie, L., Srinivas, H. et al. Nat Chem Biol (2020) 16:15-23. DOI 10.1038/s41589-019-0411-6 · PubMed

Other PDB entries of the same protein (UniProt Q66K64 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6UE5 2.61 Å, Crystal structure of full-length human DCAF15-DDB1-deltaPBP-DDA1-RBM39 in complex with…
6PAI 2.9 Å, Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and…
6Q0R 2.9 Å, Structure of DDB1-DDA1-DCAF15 complex bound to E7820 and RBM39
6Q0V 2.9 Å, Structure of DDB1-DDA1-DCAF15 complex bound to tasisulam and RBM39
6Q0W 2.9 Å, Structure of DDB1-DDA1-DCAF15 complex bound to Indisulam and RBM39
8ROY 3.1 Å, Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to compound furan 24
8ROX 3.3 Å, Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to compound furan 12
6SJ7 3.54 Å, Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and Indisulam

Browse structure collections

About this viewer

MolViewer shows 6UD7 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.