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Yorodumi- PDB-8oga: Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8oga | |||||||||
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Title | Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 6 | |||||||||
Components | DDB1- and CUL4-associated factor 1 | |||||||||
Keywords | TRANSFERASE / DCAF1 / E3 ligase / compound | |||||||||
Function / homology | Function and homology information histone H2AT120 kinase activity / cell competition in a multicellular organism / V(D)J recombination / Cul4-RING E3 ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / B cell differentiation / post-translational protein modification / nuclear estrogen receptor binding / fibrillar center / positive regulation of protein catabolic process ...histone H2AT120 kinase activity / cell competition in a multicellular organism / V(D)J recombination / Cul4-RING E3 ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / B cell differentiation / post-translational protein modification / nuclear estrogen receptor binding / fibrillar center / positive regulation of protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / non-specific serine/threonine protein kinase / protein ubiquitination / phosphorylation / protein serine kinase activity / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Schroeder, M. / Vulpetti, A. / Renatus, M. | |||||||||
Funding support | 1items
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Citation | Journal: Acs Med.Chem.Lett. / Year: 2023 Title: Discovery of New Binders for DCAF1, an Emerging Ligase Target in the Targeted Protein Degradation Field. Authors: Vulpetti, A. / Holzer, P. / Schmiedeberg, N. / Imbach-Weese, P. / Pissot-Soldermann, C. / Hollingworth, G.J. / Radimerski, T. / Thoma, C.R. / Stachyra, T.M. / Wojtynek, M. / Maschlej, M. / ...Authors: Vulpetti, A. / Holzer, P. / Schmiedeberg, N. / Imbach-Weese, P. / Pissot-Soldermann, C. / Hollingworth, G.J. / Radimerski, T. / Thoma, C.R. / Stachyra, T.M. / Wojtynek, M. / Maschlej, M. / Chau, S. / Schuffenhauer, A. / Fernandez, C. / Schroder, M. / Renatus, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oga.cif.gz | 234.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oga.ent.gz | 183.8 KB | Display | PDB format |
PDBx/mmJSON format | 8oga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8oga_validation.pdf.gz | 733.2 KB | Display | wwPDB validaton report |
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Full document | 8oga_full_validation.pdf.gz | 736 KB | Display | |
Data in XML | 8oga_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 8oga_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/8oga ftp://data.pdbj.org/pub/pdb/validation_reports/og/8oga | HTTPS FTP |
-Related structure data
Related structure data | 8og5C 8og6C 8og7C 8og8C 8og9C 8ogbC 8ogcC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36062.562 Da / Num. of mol.: 1 / Mutation: Q1250L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DCAF1, KIAA0800, RIP, VPRBP / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9Y4B6, non-specific serine/threonine protein kinase | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-VLW / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M Tris pH 7.5, 1.66M Lithium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Sep 24, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→46.96 Å / Num. obs: 24491 / % possible obs: 100 % / Redundancy: 29.5 % / CC1/2: 0.995 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.2→2.27 Å / Num. unique obs: 2058 / CC1/2: 0.703 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.191 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 12.866 / SU ML: 0.141 / Cross valid method: FREE R-VALUE / ESU R: 0.182 / ESU R Free: 0.154 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.031 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→45.191 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -14.6277 Å / Origin y: -31.8078 Å / Origin z: 11.6545 Å
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Refinement TLS group | Selection: ALL |