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Yorodumi- PDB-3ivv: Structures of SPOP-Substrate Complexes: Insights into Molecular A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ivv | ||||||
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Title | Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-PucSBC1_pep1 | ||||||
Components |
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Keywords | LIGASE / Protein Binding / Nucleus / Ubl conjugation pathway | ||||||
Function / homology | Function and homology information regulation of proteolysis / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / localization / Hedgehog 'on' state / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / nucleoplasm ...regulation of proteolysis / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / localization / Hedgehog 'on' state / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Schulman, B.A. / Miller, D.J. / Calabrese, M.F. / Seyedin, S. | ||||||
Citation | Journal: Mol.Cell / Year: 2009 Title: Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases. Authors: Zhuang, M. / Calabrese, M.F. / Liu, J. / Waddell, M.B. / Nourse, A. / Hammel, M. / Miller, D.J. / Walden, H. / Duda, D.M. / Seyedin, S.N. / Hoggard, T. / Harper, J.W. / White, K.P. / Schulman, B.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ivv.cif.gz | 82.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ivv.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ivv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/3ivv ftp://data.pdbj.org/pub/pdb/validation_reports/iv/3ivv | HTTPS FTP |
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-Related structure data
Related structure data | 3hqhC 3hqiC 3hqlC 3hqmC 3hsvC 3htmC 3hu6C 3hveC 3ivqC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16543.967 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPOP / Production host: Escherichia coli (E. coli) / References: UniProt: O43791 |
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#2: Protein/peptide | Mass: 1012.970 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 22% PME 550, 0.1 M HEPES, Cryoprotection: 30% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9794 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→50 Å / Num. all: 39304 / Num. obs: 39299 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.038 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.25→1.29 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 3926 / Rsym value: 0.276 / % possible all: 99.9 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→41.27 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.392 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.051 / 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: 14.867 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→41.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.281 Å / Total num. of bins used: 20
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