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Yorodumi- PDB-2zne: Crystal structure of Zn2+-bound form of des3-23ALG-2 complexed wi... -
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-Basic information
Entry | Database: PDB / ID: 2zne | ||||||
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Title | Crystal structure of Zn2+-bound form of des3-23ALG-2 complexed with Alix ABS peptide | ||||||
Components |
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Keywords | APOPTOSIS / PENTA-EF-HAND PROTEIN / CALCIUM BINDING PROTEIN / Endoplasmic reticulum / Membrane / Nucleus / Polymorphism / Cytoplasm / Host-virus interaction / Protein transport / Transport | ||||||
Function / homology | Function and homology information proteinase activated receptor binding / actomyosin contractile ring assembly / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / regulation of extracellular exosome assembly / neural crest formation / viral budding / extracellular exosome biogenesis / maintenance of epithelial cell apical/basal polarity / positive regulation of extracellular exosome assembly / regulation of membrane permeability ...proteinase activated receptor binding / actomyosin contractile ring assembly / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / regulation of extracellular exosome assembly / neural crest formation / viral budding / extracellular exosome biogenesis / maintenance of epithelial cell apical/basal polarity / positive regulation of extracellular exosome assembly / regulation of membrane permeability / vascular endothelial growth factor receptor-2 signaling pathway / neural crest cell development / COPII vesicle coat / regulation of centrosome duplication / COPII vesicle coating / midbody abscission / multivesicular body sorting pathway / bicellular tight junction assembly / actomyosin / positive regulation of exosomal secretion / negative regulation of TOR signaling / multivesicular body assembly / Flemming body / positive regulation of protein monoubiquitination / RIPK1-mediated regulated necrosis / Cul3-RING ubiquitin ligase complex / negative regulation of vascular endothelial growth factor receptor signaling pathway / viral budding via host ESCRT complex / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / mitotic cytokinesis / Uptake and function of anthrax toxins / ubiquitin-like ligase-substrate adaptor activity / immunological synapse / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / bicellular tight junction / 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 / macroautophagy / intracellular protein transport / Budding and maturation of HIV virion / protein homooligomerization / Regulation of necroptotic cell death / response to calcium ion / calcium-dependent protein binding / positive regulation of angiogenesis / extracellular vesicle / melanosome / protein-macromolecule adaptor activity / protein transport / cellular response to heat / cytoplasmic vesicle / angiogenesis / protein dimerization activity / endosome / focal adhesion / centrosome / apoptotic process / calcium ion binding / endoplasmic reticulum membrane / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 | 2zne.cif.gz | 88.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zne.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 2zne.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/2zne ftp://data.pdbj.org/pub/pdb/validation_reports/zn/2zne | HTTPS FTP |
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-Related structure data
Related structure data | 2zn8C 2zn9C 2zndC 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 19877.145 Da / Num. of mol.: 2 / Fragment: residues 2-191 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 #2: Protein/peptide | Mass: 1771.879 Da / Num. of mol.: 2 / Fragment: ALG-2 binding site, residues 799-814 / Mutation: C15S / Source method: obtained synthetically Details: chemical synthesis; This sequence occurs naturally in humans. References: UniProt: Q8WUM4 #3: Chemical | ChemComp-ZN / #4: Chemical | #5: 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: 2.56 Å3/Da / Density % sol: 52.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 10% 2-propanol, 0.1M Cacodylate, 0.2M zinc acetate, pH 6.5, VAPOR DIFFUSION, SITTING 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: Oct 11, 2006 |
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→50 Å / Num. obs: 23278 / % possible obs: 98 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 4 / Num. unique all: 2099 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HQV Resolution: 2.2→33.94 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.903 / SU B: 6.862 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.233 / 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: 37.722 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→33.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.198→2.255 Å / Total num. of bins used: 20
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