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- PDB-6ue5: Crystal structure of full-length human DCAF15-DDB1-deltaPBP-DDA1-... -

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Basic information

Entry
Database: PDB / ID: 6ue5
TitleCrystal structure of full-length human DCAF15-DDB1-deltaPBP-DDA1-RBM39 in complex with 4-(aminomethyl)-N-(3-cyano-4-methyl-1H-indol-7-yl)benzenesulfonamide
Components
  • DDB1- and CUL4-associated factor 15
  • DET1- and DDB1-associated protein 1
  • DNA damage-binding protein 1,DNA damage-binding protein 1
  • RBM39
KeywordsLIGASE / E3 ligase / neosubstrate
Function / homology
Function and homology information


RS domain binding / U1 snRNP binding / regulation of mRNA splicing, via spliceosome / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cytokinesis / regulation of mitotic cell cycle phase transition ...RS domain binding / U1 snRNP binding / regulation of mRNA splicing, via spliceosome / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cytokinesis / regulation of mitotic cell cycle phase transition / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation / small molecule binding / WD40-repeat domain binding / regulation of cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / regulation of stem cell population maintenance / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of adipose tissue development / regulation of cellular response to stress / viral release from host cell / cullin family protein binding / regulation of DNA-templated DNA replication initiation / RNA processing / positive regulation of viral genome replication / positive regulation of gluconeogenesis / immune system process / mRNA Splicing - Major Pathway / RNA splicing / regulation of embryonic development / replication fork processing / proteasomal protein catabolic process / epigenetic regulation of gene expression / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / regulation of autophagy / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / cell population proliferation / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / mRNA processing / mRNA Polyadenylation / protein polyubiquitination / Formation of Incision Complex in GG-NER / positive regulation of protein catabolic process / cellular response to UV / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of cell population proliferation / rhythmic process / site of double-strand break / Neddylation / spermatogenesis / ubiquitin-dependent protein catabolic process / damaged DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of apoptotic process / protein-macromolecule adaptor activity / chromosome, telomeric region / nuclear speck / protein ubiquitination / DNA repair / DNA damage response / nucleolus / protein-containing complex binding / protein-containing complex / DNA binding / : / DNA-templated transcription / RNA binding / extracellular exosome / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
DDB1- and CUL4-associated factor 15, WD40 repeat-containing domain / DDB1- and CUL4-associated factor 15 / : / DDB1-and CUL4-substrate receptor 15, WD repeat / Splicing factor, RBM39-like / Splicing factor RBM39, linker / linker between RRM2 and RRM3 domains in RBM39 protein / DET1- and DDB1-associated protein 1, N-terminal / DET1- and DDB1-associated protein 1 / Det1 complexing ubiquitin ligase ...DDB1- and CUL4-associated factor 15, WD40 repeat-containing domain / DDB1- and CUL4-associated factor 15 / : / DDB1-and CUL4-substrate receptor 15, WD repeat / Splicing factor, RBM39-like / Splicing factor RBM39, linker / linker between RRM2 and RRM3 domains in RBM39 protein / DET1- and DDB1-associated protein 1, N-terminal / DET1- and DDB1-associated protein 1 / Det1 complexing ubiquitin ligase / DNA polymerase; domain 1 - #910 / RNA recognition motif domain, eukaryote / RNA recognition motif / : / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / RRM (RNA recognition motif) domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / DNA polymerase; domain 1 / Alpha-Beta Plaits / Nucleotide-binding alpha-beta plait domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-Q5J / RNA-binding protein 39 / DNA damage-binding protein 1 / DDB1- and CUL4-associated factor 15 / Uncharacterized protein DKFZp781I1140 / DET1- and DDB1-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.61 Å
AuthorsKnapp, M.S. / Shu, W. / Xie, L. / Bussiere, D.E.
CitationJournal: Nat Chem Biol / Year: 2020
Title: Structural basis of indisulam-mediated RBM39 recruitment to DCAF15 E3 ligase complex.
Authors: Dirksen E Bussiere / Lili Xie / Honnappa Srinivas / Wei Shu / Ashley Burke / Celine Be / Junping Zhao / Adarsh Godbole / Dan King / Rajeshri G Karki / Viktor Hornak / Fangmin Xu / Jennifer ...Authors: Dirksen E Bussiere / Lili Xie / Honnappa Srinivas / Wei Shu / Ashley Burke / Celine Be / Junping Zhao / Adarsh Godbole / Dan King / Rajeshri G Karki / Viktor Hornak / Fangmin Xu / Jennifer Cobb / Nathalie Carte / Andreas O Frank / Alexandra Frommlet / Patrick Graff / Mark Knapp / Aleem Fazal / Barun Okram / Songchun Jiang / Pierre-Yves Michellys / Rohan Beckwith / Hans Voshol / Christian Wiesmann / Jonathan M Solomon / Joshiawa Paulk /
Abstract: The anticancer agent indisulam inhibits cell proliferation by causing degradation of RBM39, an essential mRNA splicing factor. Indisulam promotes an interaction between RBM39 and the DCAF15 E3 ligase ...The anticancer agent indisulam inhibits cell proliferation by causing degradation of RBM39, an essential mRNA splicing factor. Indisulam promotes an interaction between RBM39 and the DCAF15 E3 ligase substrate receptor, leading to RBM39 ubiquitination and proteasome-mediated degradation. To delineate the precise mechanism by which indisulam mediates the DCAF15-RBM39 interaction, we solved the DCAF15-DDB1-DDA1-indisulam-RBM39(RRM2) complex structure to a resolution of 2.3 Å. DCAF15 has a distinct topology that embraces the RBM39(RRM2) domain largely via non-polar interactions, and indisulam binds between DCAF15 and RBM39(RRM2), coordinating additional interactions between the two proteins. Studies with RBM39 point mutants and indisulam analogs validated the structural model and defined the RBM39 α-helical degron motif. The degron is found only in RBM23 and RBM39, and only these proteins were detectably downregulated in indisulam-treated HCT116 cells. This work further explains how indisulam induces RBM39 degradation and defines the challenge of harnessing DCAF15 to degrade additional targets.
History
DepositionSep 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DDB1- and CUL4-associated factor 15
B: DNA damage-binding protein 1,DNA damage-binding protein 1
C: RBM39
D: DET1- and DDB1-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,1526
Polymers180,7204
Non-polymers4322
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14510 Å2
ΔGint-66 kcal/mol
Surface area59050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.692, 94.237, 267.578
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein DDB1- and CUL4-associated factor 15


Mass: 66563.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCAF15, C19orf72 / Production host: Escherichia coli (E. coli) / References: UniProt: Q66K64
#2: Protein DNA damage-binding protein 1,DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 93347.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16531
#3: Protein RBM39


Mass: 9085.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp781I1140 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z3L0, UniProt: Q14498*PLUS
#4: Protein DET1- and DDB1-associated protein 1 / Placenta cross-immune reaction antigen 1 / PCIA-1


Mass: 11724.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDA1, C19orf58, PCIA1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BW61

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Non-polymers , 3 types, 517 molecules

#5: Chemical ChemComp-Q5J / 4-(aminomethyl)-N-(3-cyano-4-methyl-1H-indol-7-yl)benzene-1-sulfonamide


Mass: 340.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16N4O2S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2% (v:v) TacsimateTM, pH 5.0, 0.1 M sodium citrate tribasic 676 dihydrate, pH 5.6, and 10-20% (w:v) polyethylene glycol 3350
PH range: 5-5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Aug 17, 2018
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.61→81.79 Å / Num. obs: 63346 / % possible obs: 100 % / Redundancy: 19.6 % / Biso Wilson estimate: 44.13 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.487 / Rpim(I) all: 0.113 / Rrim(I) all: 0.5 / Net I/σ(I): 6.2
Reflection shellResolution: 2.61→2.69 Å / Redundancy: 19.3 % / Rmerge(I) obs: 3.221 / Num. unique obs: 4597 / CC1/2: 0.326 / Rpim(I) all: 0.752 / Rrim(I) all: 3.309 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
Aimless0.7.3data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UD7

6ud7


Resolution: 2.61→78.13 Å / Cor.coef. Fo:Fc: 0.867 / Cor.coef. Fo:Fc free: 0.833 / SU R Cruickshank DPI: 0.49 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.512 / SU Rfree Blow DPI: 0.292 / SU Rfree Cruickshank DPI: 0.293
RfactorNum. reflection% reflectionSelection details
Rfree0.266 3190 5.04 %RANDOM
Rwork0.239 ---
obs0.241 63255 99.6 %-
Displacement parametersBiso max: 273.4 Å2 / Biso mean: 75.62 Å2 / Biso min: 13.19 Å2
Baniso -1Baniso -2Baniso -3
1-16.4534 Å20 Å20 Å2
2---9.0551 Å20 Å2
3----7.3984 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å
Refinement stepCycle: final / Resolution: 2.61→78.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10698 0 30 515 11243
Biso mean--44.12 51.08 -
Num. residues----1377
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3738SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1880HARMONIC5
X-RAY DIFFRACTIONt_it10976HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1437SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11522SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10976HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg14892HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion2.19
X-RAY DIFFRACTIONt_other_torsion16.34
LS refinement shellResolution: 2.61→2.63 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2489 68 5.37 %
Rwork0.2249 1198 -
all0.2263 1266 -
obs--85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.52351.082-2.38323.5583-0.33362.4790.1244-1.51140.52010.92420.08060.1004-0.46240.2241-0.20490.59190.2035-0.21020.96250.34180.4881-4.412812.28436.8394
23.2534-0.04310.63339.0564-3.5114.7971-0.2235-0.28560.02991.19390.44881.5159-0.2791-1.2801-0.22540.46090.01390.12880.77-0.07160.6237-27.2575-6.408954.427
33.1191-1.19250.6462.3088-0.83952.0832-0.0314-0.0764-0.53890.04090.07010.95280.6091-0.9618-0.03860.696-0.32380.03380.6256-0.03450.8233-20.6344-18.691255.7474
43.1984-1.3398-0.85262.9367-0.34350.43540.1460.9127-0.9136-0.5172-0.28450.8030.7993-0.37480.13860.9098-0.1628-0.01970.3542-0.07510.6193-6.7663-27.74147.8555
52.427-0.99670.0792.2056-0.37381.7785-0.03440.1801-0.9877-0.44260.00020.53350.8621-0.51560.03411.1193-0.17270.10660.30530.0610.7637-4.8275-32.45253.9203
61.952-0.5052-0.17863.5681-0.82772.1155-0.0074-0.0177-0.07390.2653-0.3382-0.37210.470.44440.34550.7516-0.07220.11270.32770.15670.43148.676-21.501764.1634
72.3163-0.26730.83976.4539-2.86911.5664-0.2441-0.4366-0.32160.5652-0.05010.4387-0.3960.05590.29410.5741-0.05790.0290.3758-0.00870.6609-17.2811-0.010254.2016
83.46380.0542-0.52432.3571-0.73053.0257-0.06370.11070.07720.0906-0.3126-0.49550.10630.9640.37640.29050.14550.04320.93180.5480.296418.91475.744328.0637
93.9669-0.5085-0.81322.3656-0.34312.3745-0.02250.54160.2092-0.0138-0.00780.3352-0.0287-0.61650.03040.26010.107-0.08280.84350.25740.3025-13.062411.637320.456
107.4143-3.6626-1.43465.16654.39214.3157-0.0820.8047-0.1343-1.01660.1074-0.35350.1907-0.0185-0.02551.44040.2139-0.06782.0253-0.40270.7014-3.2061-17.302-6.3212
117.6144-2.95840.55753.9861-4.88517.7148-0.75471.15490.50020.08690.1126-0.197-0.79510.68020.64221.4727-0.2747-0.00521.3776-0.02510.4539-5.9414-4.2299-0.7346
123.3807-0.22552.14977.65591.72923.8840.1012-0.12350.70120.4991-0.0805-0.0033-0.6572-0.1417-0.02080.7385-0.05640.04020.3196-0.06210.4762-3.6028-1.826369.3644
130.89961.17290.28815.4941-1.06395.50930.04190.02670.36880.484-0.23320.6613-0.4683-0.40680.19140.6423-0.10290.14330.1536-0.06190.5752-6.9783-10.372570.1163
144.9306-2.25231.78382.85081.36473.2686-0.20160.21220.43830.964-0.20010.1097-0.586-0.18040.40180.8424-0.11140.09550.3127-0.0440.5027-2.307-3.092470.8522
158.0552-5.181-4.01823.33112.39987.22630.1715-0.21920.77860.8916-0.02540.9504-0.8648-0.4587-0.14610.7159-0.09850.16710.4233-0.0460.7512-5.18051.395777.9694
165.09890.5986-2.03285.1271.22853.41820.0038-0.00250.2933-0.27390.0401-0.3243-0.4079-0.2966-0.0440.2526-0.03550.20051.64960.63330.777933.149715.929814.6928
179.97384.3085-3.27448.0742-1.96163.8022-0.15290.48692.5652-1.0547-0.35361.0671-1.0105-0.66390.50651.08690.14420.05111.76720.32040.950816.301318.55124.1229
182.99590.1490.91211.8296-2.52426.59290.24290.8739-0.3754-0.6443-0.1356-0.26640.64140.6445-0.10720.73810.34910.16741.16060.0660.768914.8801-13.265518.5854
192.76581.5019-3.11692.6602-0.29954.58130.0234-1.0024-0.91920.8185-0.3044-1.35170.45791.41160.28090.87790.34-0.13530.84670.651.420623.1533-23.486256.1983
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|32 - A|60 }A32 - 60
2X-RAY DIFFRACTION2{ A|61 - A|105 }A61 - 105
3X-RAY DIFFRACTION3{ A|106 - A|232 }A106 - 232
4X-RAY DIFFRACTION4{ A|233 - A|388 }A233 - 388
5X-RAY DIFFRACTION5{ A|389 - A|486 }A389 - 486
6X-RAY DIFFRACTION6{ A|487 - A|575 }A487 - 575
7X-RAY DIFFRACTION7{ A|576 - A|600 }A576 - 600
8X-RAY DIFFRACTION8{ B|2 - B|385 }B2 - 385
9X-RAY DIFFRACTION9{ B|386 - B|1110 }B386 - 1110
10X-RAY DIFFRACTION10{ B|1125 - B|1130 }B1125 - 1130
11X-RAY DIFFRACTION11{ B|1131 - B|1140 }B1131 - 1140
12X-RAY DIFFRACTION12{ C|248 - C|262 }C248 - 262
13X-RAY DIFFRACTION13{ C|263 - C|281 }C263 - 281
14X-RAY DIFFRACTION14{ C|282 - C|321 }C282 - 321
15X-RAY DIFFRACTION15{ C|322 - C|328 }C322 - 328
16X-RAY DIFFRACTION16{ D|4 - D|18 }D4 - 18
17X-RAY DIFFRACTION17{ D|19 - D|28 }D19 - 28
18X-RAY DIFFRACTION18{ D|29 - D|53 }D29 - 53
19X-RAY DIFFRACTION19{ D|54 - D|76 }D54 - 76

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