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Yorodumi- PDB-8oo5: Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex... -
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-Basic information
Entry | Database: PDB / ID: 8oo5 | ||||||
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Title | Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 13 | ||||||
Components | DDB1- and CUL4-associated factor 1 | ||||||
Keywords | TRANSFERASE / DCAF1 / 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: 2.25 Å | ||||||
Authors | Schroeder, M. / Renatus, M. | ||||||
Funding support | 1items
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Citation | Journal: Biorxiv / Year: 2023 Title: Reinstating targeted protein degradation with DCAF1 PROTACs in CRBN PROTAC resistant settings Authors: Schroder, M. / Renatus, M. / Thoma, C.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oo5.cif.gz | 142.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oo5.ent.gz | 109 KB | Display | PDB format |
PDBx/mmJSON format | 8oo5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8oo5_validation.pdf.gz | 974.1 KB | Display | wwPDB validaton report |
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Full document | 8oo5_full_validation.pdf.gz | 983.1 KB | Display | |
Data in XML | 8oo5_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 8oo5_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/8oo5 ftp://data.pdbj.org/pub/pdb/validation_reports/oo/8oo5 | HTTPS FTP |
-Related structure data
Related structure data | 8oodC 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 | ChemComp-EDO / #4: 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: 3.12 Å3/Da / Density % sol: 60.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.91M LiSO4, 0.1M Tris pH 7.5 |
-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 X 16M / Detector: PIXEL / Date: Oct 12, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→52.43 Å / Num. obs: 22902 / % possible obs: 100 % / Redundancy: 21.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.271 / Rpim(I) all: 0.059 / Rrim(I) all: 0.278 / Χ2: 0.97 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.25→2.32 Å / % possible obs: 100 % / Redundancy: 22.9 % / Rmerge(I) obs: 2.748 / Num. measured all: 47398 / Num. unique obs: 2066 / CC1/2: 0.771 / Rpim(I) all: 0.583 / Rrim(I) all: 2.81 / Χ2: 0.96 / Net I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→52.43 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 11.19 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.928 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→52.43 Å
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