6SJ7: Human DDB1-DDA1-DCAF15 E3 ubiquitin ligase

Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and Indisulam. Determined by electron microscopy at 3.54 Å resolution. Released 18 Dec 2019.

Method: Electron microscopy
Resolution: 3.54 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,007
Mol. weight: 214.86 kDa
Ligands: EF6
Released: 18 Dec 2019

Explore 6SJ7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6SJ7 contains 23 α-helices and 106 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: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	37-46	10
α-helix	58-59	2
β-strand	61-63	3	1
β-strand	79-83	5	2
β-strand	89-94	6	2
β-strand	108-113	6	2
β-strand	121-127	7	2
β-strand	139-144	6	3
β-strand	151-157	7	3
β-strand	178-186	9	3
α-helix	187-189	3
β-strand	217-224	8	3
α-helix	229-231	3
β-strand	242-246	5	4
β-strand	250-258	9	4
β-strand	421-423	3	3
β-strand	441-449	9	4
α-helix	450-460	11
β-strand	470-471	2	5
β-strand	475-482	8	6
β-strand	487-493	7	6
β-strand	495-497	3	5
β-strand	512-514	3	5
β-strand	517-522	6	6
β-strand	529-533	5	6
β-strand	538-539	2	5
α-helix	546-561	16
α-helix	566-567	2
α-helix	572-573	2
β-strand	574-575	2	3
β-strand	589-591	3	1
β-strand	596-598	3	1

Chain B: 10 helices, 73 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	7
β-strand	17-21	5	8
β-strand	30-35	6	8
β-strand	38-44	7	8
β-strand	49-51	3	8
β-strand	55-56	2	8
β-strand	61-67	7	9
β-strand	76-81	6	9
β-strand	85-90	6	9
β-strand	93-94	2	10
β-strand	97-98	2	10
β-strand	101-107	7	9
β-strand	115	1	11
β-strand	121-124	4	12
β-strand	130-134	5	12
β-strand	136	1	11
β-strand	140-144	5	12
β-strand	151-154	4	9
β-strand	155-157	3	12
β-strand	164-169	6	13
α-helix	170	1
β-strand	177-182	6	13
β-strand	189-196	8	13
β-strand	201-204	4	13
β-strand	210-211	2	13
β-strand	218-221	4	14
β-strand	229-232	4	14
β-strand	237-241	5	14
β-strand	244-246	3	14
α-helix	253-255	3
β-strand	258-263	6	15
β-strand	270-275	6	15
β-strand	279-284	6	15
β-strand	287-288	2	16
β-strand	296-297	2	16
β-strand	301-307	7	15
β-strand	311-313	3	17
β-strand	316-317	2	18
α-helix	318-320	3
β-strand	321-324	4	18
β-strand	325-326	2	17
β-strand	331-336	6	18
β-strand	347-353	7	18
β-strand	362-365	4	19
β-strand	374-379	6	19
β-strand	386-391	6	19
β-strand	711-716	6	19
β-strand	720-727	8	20
β-strand	732-743	12	20
β-strand	749-751	3	20
α-helix	757-759	3
β-strand	762-765	4	20
β-strand	786-795	10	20
β-strand	801-806	6	20
β-strand	811-819	9	21
β-strand	828-835	8	21
β-strand	845-853	9	21
β-strand	858-866	9	21
β-strand	872-875	4	22
β-strand	880-883	4	22
β-strand	888-893	6	22
β-strand	899-905	7	22
β-strand	911-917	7	23
β-strand	920-925	6	23
β-strand	931-934	4	23
β-strand	943-947	5	23
β-strand	954-959	6	24
β-strand	965-969	5	24
β-strand	973-979	7	24
α-helix	986-989	4
β-strand	992-998	7	24
β-strand	1004-1009	6	7
β-strand	1028-1032	5	7
β-strand	1037-1042	6	7
α-helix	1046-1058	13
α-helix	1070-1073	4
β-strand	1076-1077	2	25
β-strand	1082-1083	2	25
β-strand	1086	1	24
β-strand	1088-1090	3	7
α-helix	1091-1095	5
α-helix	1102-1108	7
α-helix	1127-1136	10

Chain C: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	251-253	3	26
α-helix	263-270	8
α-helix	271-273	3
β-strand	276-280	5	26
β-strand	283-284	2	27
β-strand	289-290	2	27
β-strand	295-298	4	26
α-helix	303-310	8
β-strand	314-316	3	28
β-strand	319-321	3	28
β-strand	324	1	26

Chain D: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	32-34	3
β-strand	45-49	5	9
α-helix	54-63	10

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	B	protein	1140	Homo sapiens	Q16531 (AlphaFold model)
RNA binding 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

>6SJ7_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

>6SJ7_2 DNA damage-binding protein 1 (chains B)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 3 (C), FASTA

>6SJ7_3 RNA binding protein 39 (chains C)
GPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKA
LEQLNGFELAGRPMKVGHVTE

Sequence of entity 4 (D), FASTA

>6SJ7_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

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:

6UD7 2.3 Å, Crystal structure of full-length human DCAF15-DDB1(deltaBPB)-DDA1-RBM39 in complex with…
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

Browse structure collections

About this viewer

MolViewer shows 6SJ7 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.