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

Name: PDB 6PAI: Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and sulfonamide E7820
Published: 2019-09-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and sulfonamide E7820. Determined by X-ray diffraction at 2.9 Å resolution. Released 18 Sept 2019.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 13,196
Mol. weight: 208.34 kDa
Ligands: ZN, O6M
Released: 18 Sept 2019

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

Secondary structure: helices and β-sheets

6PAI contains 40 α-helices and 133 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: 20 helices, 98 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	38-44	7	2
β-strand	49-56	8	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	210-211	2	5
β-strand	218-221	4	6
β-strand	229-232	4	6
β-strand	237-240	4	6
β-strand	245-248	4	6
α-helix	251-254	4
β-strand	258-263	6	7
β-strand	270-275	6	7
β-strand	279-289	11	7
β-strand	295-307	13	7
α-helix	310-311	2
β-strand	313-316	4	8
β-strand	321-325	5	8
β-strand	331-336	6	8
α-helix	337	1
β-strand	347-353	7	8
α-helix	357	1
β-strand	359-365	7	9
β-strand	374-379	6	9
α-helix	382-384	3
β-strand	386-392	7	9
β-strand	394	1	10
β-strand	396-403	8	11
β-strand	409-413	5	12
β-strand	424-428	5	12
β-strand	433-437	5	12
β-strand	445-446	2	12
β-strand	457-463	7	13
β-strand	467-472	6	13
β-strand	476-479	4	13
β-strand	486-490	5	13
α-helix	496-498	3
β-strand	500-503	4	14
β-strand	507-512	6	14
β-strand	515-522	8	14
β-strand	525-533	9	14
β-strand	538-542	5	15
α-helix	544-546	3
β-strand	555-560	6	15
β-strand	565-570	6	15
β-strand	576-581	6	15
β-strand	588-595	8	16
β-strand	600-606	7	16
β-strand	610-616	7	16
β-strand	623-630	8	16
α-helix	635-636	2
β-strand	637-643	7	17
β-strand	646-652	7	17
β-strand	657-662	6	17
β-strand	665-670	6	17
β-strand	671	1	10
β-strand	678-682	5	11
β-strand	690-694	5	11
β-strand	698-704	7	11
α-helix	705	1
β-strand	710-716	7	9
β-strand	720-727	8	18
β-strand	732-742	11	18
β-strand	750-751	2	18
α-helix	756-758	3
β-strand	762-765	4	18
β-strand	785-795	11	18
β-strand	801-806	6	18
β-strand	811-819	9	19
β-strand	828-835	8	19
β-strand	846-854	9	19
β-strand	857-866	10	19
β-strand	870-876	7	20
β-strand	879-884	6	20
β-strand	887-893	7	20
β-strand	899-905	7	20
β-strand	911-917	7	21
β-strand	920-925	6	21
β-strand	928	1	22
β-strand	930-936	7	21
β-strand	941-947	7	21
β-strand	952	1	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	21
β-strand	992-999	8	23
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	1070-1073	4
β-strand	1076-1077	2	24
β-strand	1082-1083	2	24
β-strand	1086	1	23
β-strand	1088-1090	3	1
α-helix	1091-1095	5
α-helix	1096-1098	3
α-helix	1102-1108	7
α-helix	1126-1136	11
α-helix	1137-1139	3

Chain C: 13 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	36-46	11
α-helix	54-56	3
α-helix	58-59	2
β-strand	61-64	4	25
α-helix	65-67	3
β-strand	79-83	5	26
β-strand	89-96	8	26
β-strand	105	1	27
β-strand	106-115	10	26
β-strand	118-128	11	26
β-strand	134	1	27
α-helix	137-138	2
β-strand	139-144	6	28
β-strand	151-157	7	28
β-strand	177-186	10	28
α-helix	194-199	6
β-strand	217-225	9	28
α-helix	228-231	4
α-helix	233-236	4
β-strand	242-246	5	29
β-strand	250-259	10	29
β-strand	388	1	29
β-strand	392-395	4	29
β-strand	417-420	4	28
α-helix	425	1
β-strand	426	1	28
α-helix	427	1
β-strand	428-429	2	29
β-strand	440-449	10	29
α-helix	450-460	11
β-strand	468-482	15	30
β-strand	487-498	12	30
β-strand	511-522	12	30
β-strand	528-533	6	30
β-strand	537-538	2	30
α-helix	544-562	19
α-helix	571-572	2
β-strand	573-575	3	28
β-strand	588-590	3	25
β-strand	596-599	4	25

Chain D: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	250-255	6	31
α-helix	263-270	8
α-helix	271-273	3
β-strand	276-283	8	31
β-strand	290-298	9	31
α-helix	301-311	11
β-strand	314-316	3	32
β-strand	319-321	3	32
β-strand	322-325	4	31

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	32-33	2
β-strand	34-35	2	2
α-helix	41-43	3
β-strand	45-49	5	3
α-helix	54-64	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A	protein	1140	Homo sapiens	Q16531 (AlphaFold model)
DDB1- and CUL4-associated factor 15	C	protein	498	Homo sapiens	Q66K64 (AlphaFold model)
RNA-binding protein 39	D	protein	109	Homo sapiens	Q14498 (AlphaFold model)
DET1- and DDB1-associated protein 1	E	protein	102	Homo sapiens	Q9BW61 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6PAI_1 DNA damage-binding protein 1 (chains A)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 2 (C), FASTA

>6PAI_2 DDB1- and CUL4-associated factor 15 (chains C)
MHHHHHHAPSSKSERNSGAGSGGGGPGGAGGKRAAGRRREHVLKQLERVKISGQLSPRLF
RKLPPRVCVSLKNIVDEDFLYAGHIFLGFSKCGRYVLSYTSSSGDDDFSFYIYHLYWWEF
NVHSKLKLVRQVRLFQDEEIYSDLYLTVCEWPSDASKVIVFGFNTRSANGMLMNMMMMSD
ENHRDIYVSTVAVPPPGRCAACQDASRAHPGDPNAQCLRHGFMLHTKYQVVYPFPTFQPA
FQLKKDQVVLLNTSYSLVACAVSVHSAGDRSFCQILYDHSTPGYVNYTKLYYVLESGEGT
EPEDELEDDKISLPFVVTDLRGRNLRPMRERTAVQGQYLTVEQLTLDFEYVINEVIRHDA
TWGHQFCSFSDYDIVILEVCPETNQVLINIGLLLLAFPSPTEEGQLRPKTYHTSLKVAWD
LNTGIFETVSVGDLTEVKGQTSGSVWSSYRKSCVDMVMKWLVPESSGRYVNRMTNEALHK
GCSLKVLADSERYTWIVL

Sequence of entity 3 (D), FASTA

>6PAI_3 RNA-binding protein 39 (chains D)
GSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRS
KGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTDDYKDDDDK

Sequence of entity 4 (E), FASTA

>6PAI_4 DET1- and DDB1-associated protein 1 (chains E)
MADFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLH
QQWDKKNAAKKRDQEQVELEGESSAPPRKVARTDSPDMHEDT

Ligands and cofactors

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

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

Primary citation

Structural Basis and Kinetic Pathway of RBM39 Recruitment to DCAF15 by a Sulfonamide Molecular Glue E7820. Du, X., Volkov, O.A., Czerwinski, R.M. et al. Structure (2019) 27:1625-1633.e3. DOI 10.1016/j.str.2019.10.005 · 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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