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Yorodumi- PDB-6ud7: Crystal structure of full-length human DCAF15-DDB1(deltaBPB)-DDA1... -
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-Basic information
Entry | Database: PDB / ID: 6ud7 | ||||||
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Title | Crystal structure of full-length human DCAF15-DDB1(deltaBPB)-DDA1-RBM39 in complex with indisulam | ||||||
Components |
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Keywords | LIGASE / E3 ligase / neosubstrate | ||||||
Function / homology | Function and homology information RS domain binding / regulation of natural killer cell activation / positive regulation by virus of viral protein levels in host cell / U1 snRNP binding / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / regulation of mRNA splicing, via spliceosome / biological process involved in interaction with symbiont ...RS domain binding / regulation of natural killer cell activation / positive regulation by virus of viral protein levels in host cell / U1 snRNP binding / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / regulation of mRNA splicing, via spliceosome / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / immune system process / negative regulation of reproductive process / negative regulation of developmental process / cullin family protein binding / small molecule binding / centriolar satellite / viral release from host cell / ectopic germ cell programmed cell death / positive regulation of viral genome replication / RNA processing / positive regulation of gluconeogenesis / mRNA Splicing - Major Pathway / RNA splicing / proteasomal protein catabolic process / Recognition of DNA damage by PCNA-containing replication complex / nucleotide-excision repair / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / mRNA processing / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / protein polyubiquitination / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / microtubule cytoskeleton / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / nuclear speck / DNA repair / apoptotic process / DNA damage response / protein-containing complex binding / nucleolus / negative regulation of apoptotic process / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / nucleoplasm / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Bussiere, D.E. / Shu, W. / Xie, L. / Knapp, M. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ud7.cif.gz | 589.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ud7.ent.gz | 489.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ud7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/6ud7 ftp://data.pdbj.org/pub/pdb/validation_reports/ud/6ud7 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 4 types, 4 molecules ABCD
#1: Protein | 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q66K64 |
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#2: Protein | 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531 |
#3: Protein | 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 | 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BW61 |
-Non-polymers , 3 types, 747 molecules
#5: Chemical | #6: Chemical | ChemComp-EF6 / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.79 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 2% (v:v) TacsimateTM, pH 5.0, 0.1 M sodium citrate tribasic dihydrate, pH 5.6, and 10-20% (w:v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→88.39 Å / Num. obs: 90574 / % possible obs: 99.8 % / Redundancy: 11.8 % / Biso Wilson estimate: 58.69 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.248 / Rpim(I) all: 0.076 / Rrim(I) all: 0.262 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 11.7 % / Rmerge(I) obs: 3.598 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4436 / CC1/2: 0.483 / % possible all: 98.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→69.1 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.899 / SU R Cruickshank DPI: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.252 / SU Rfree Blow DPI: 0.206 / SU Rfree Cruickshank DPI: 0.204
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Displacement parameters | Biso max: 256.26 Å2 / Biso mean: 80.55 Å2 / Biso min: 35.01 Å2
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Refine analyze | Luzzati coordinate error obs: 0.37 Å | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→69.1 Å
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LS refinement shell | Resolution: 2.3→2.31 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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