+Open data
-Basic information
Entry | Database: PDB / ID: 2zn8 | ||||||
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Title | Crystal structure of Zn2+-bound form of ALG-2 | ||||||
Components | Programmed cell death protein 6 | ||||||
Keywords | APOPTOSIS / PENTA-EF-HAND PROTEIN / CALCIUM BINDING PROTEIN / Calcium / Endoplasmic reticulum / Membrane / Nucleus / Polymorphism | ||||||
Function / homology | Function and homology information neural crest formation / vascular endothelial growth factor receptor-2 signaling pathway / neural crest cell development / COPII vesicle coat / COPII vesicle coating / negative regulation of TOR signaling / positive regulation of protein monoubiquitination / Cul3-RING ubiquitin ligase complex / negative regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process ...neural crest formation / vascular endothelial growth factor receptor-2 signaling pathway / neural crest cell development / COPII vesicle coat / COPII vesicle coating / negative regulation of TOR signaling / positive regulation of protein monoubiquitination / Cul3-RING ubiquitin ligase complex / negative regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / ubiquitin-like ligase-substrate adaptor activity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / protein-membrane adaptor activity / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / apoptotic signaling pathway / intracellular protein transport / response to calcium ion / calcium-dependent protein binding / positive regulation of angiogenesis / protein-macromolecule adaptor activity / cellular response to heat / cytoplasmic vesicle / angiogenesis / protein dimerization activity / endosome / calcium ion binding / endoplasmic reticulum membrane / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Suzuki, H. / Kawasaki, M. / Inuzuka, T. / Kakiuchi, T. / Shibata, H. / Wakatsuki, S. / Maki, M. | ||||||
Citation | Journal: Structure / Year: 2008 Title: Structural Basis for Ca(2+)-Dependent Formation of ALG-2/Alix Peptide Complex: Ca(2+)/EF3-Driven Arginine Switch Mechanism Authors: Suzuki, H. / Kawasaki, M. / Inuzuka, T. / Okumura, M. / Kakiuchi, T. / Shibata, H. / Wakatsuki, S. / Maki, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zn8.cif.gz | 48.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zn8.ent.gz | 33.8 KB | Display | PDB format |
PDBx/mmJSON format | 2zn8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/2zn8 ftp://data.pdbj.org/pub/pdb/validation_reports/zn/2zn8 | HTTPS FTP |
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-Related structure data
Related structure data | 2zn9C 2zndC 2zneC 1hqvS C: citing same article (ref.) S: Starting model for refinement |
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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: 21758.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD6, ALG2 / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O75340 | ||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NA / | #4: 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: 3.25 Å3/Da / Density % sol: 62.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% 2-methyl-2,4-pentanediol, 100mM Cacodylate, 75mM Zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 8147 / % possible obs: 98.35 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 14.1 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HQV Resolution: 2.7→32.1 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.882 / SU B: 10.725 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.49 / ESU R Free: 0.309 / 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: 42.63 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→32.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.702→2.772 Å / Total num. of bins used: 20
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