+Open data
-Basic information
Entry | Database: PDB / ID: 4emo | ||||||
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Title | Crystal structure of the PH domain of SHARPIN | ||||||
Components | SharpinLloyd Sharpin | ||||||
Keywords | PROTEIN BINDING / Pleckstrin homology (PH) domain / LUBAC / SIPL1 / linear ubiquitin / HOIL-1L / HOIP | ||||||
Function / homology | Function and homology information apoptotic nuclear changes / regulation of CD40 signaling pathway / protein linear polyubiquitination / LUBAC complex / regulation of tumor necrosis factor-mediated signaling pathway / Neurexins and neuroligins / TNFR1-induced proapoptotic signaling / keratinization / polyubiquitin modification-dependent protein binding / mitochondrion organization ...apoptotic nuclear changes / regulation of CD40 signaling pathway / protein linear polyubiquitination / LUBAC complex / regulation of tumor necrosis factor-mediated signaling pathway / Neurexins and neuroligins / TNFR1-induced proapoptotic signaling / keratinization / polyubiquitin modification-dependent protein binding / mitochondrion organization / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / Regulation of TNFR1 signaling / negative regulation of inflammatory response / ubiquitin-protein transferase activity / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / synapse / dendrite / protein-containing complex binding / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Stieglitz, B. / Haire, L.F. / Dikic, I. / Rittinger, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structural Analysis of SHARPIN, a Subunit of a Large Multi-protein E3 Ubiquitin Ligase, Reveals a Novel Dimerization Function for the Pleckstrin Homology Superfold. Authors: Stieglitz, B. / Haire, L.F. / Dikic, I. / Rittinger, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4emo.cif.gz | 89.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4emo.ent.gz | 73.4 KB | Display | PDB format |
PDBx/mmJSON format | 4emo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/4emo ftp://data.pdbj.org/pub/pdb/validation_reports/em/4emo | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13355.524 Da / Num. of mol.: 4 / Mutation: L21M, L101M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PSEC0216, SHARPIN, SIPL1 / Plasmid: pGex4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H0F6 #2: Water | ChemComp-HOH / | |
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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: 1.98 Å3/Da / Density % sol: 37.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 4M sodium formate, pH 7.4, vapor diffusion, sitting drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 77 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9799 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC / Detector: CCD / Date: May 29, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9799 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.9 % / Av σ(I) over netI: 17.17 / Number: 213897 / Rmerge(I) obs: 0.071 / Χ2: 0.95 / D res high: 2 Å / D res low: 30 Å / Num. obs: 55100 / % possible obs: 99.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2→30 Å / Num. obs: 29888 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.071 / Χ2: 0.949 / Net I/σ(I): 10.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SAD | |||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing dm | FOM : 0.73 / FOM acentric: 0.76 / FOM centric: 0.62 / Reflection: 17560 / Reflection acentric: 14320 / Reflection centric: 3240 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.2697 / WRfactor Rwork: 0.2091 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8012 / SU B: 4.362 / SU ML: 0.125 / SU R Cruickshank DPI: 0.1973 / SU Rfree: 0.1864 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.186 / 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 max: 94.58 Å2 / Biso mean: 34.5554 Å2 / Biso min: 14.85 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.048 Å / Total num. of bins used: 20
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