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- PDB-3wxa: X-ray crystal structural analysis of the complex between ALG-2 an... -
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Basic information
Entry | Database: PDB / ID: 3wxa | ||||||
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Title | X-ray crystal structural analysis of the complex between ALG-2 and Sec31A peptide | ||||||
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![]() | APOPTOSIS/TRANSPORT PROTEIN / PENTA-EF-HAND PROTEIN / Endoplasmic reticulum / Membrane / Transport / Apoptosis / Calcium Binding / APOPTOSIS-TRANSPORT PROTEIN complex | ||||||
Function / homology | ![]() vesicle coat / neural crest formation / COPII-coated vesicle cargo loading / vascular endothelial growth factor receptor-2 signaling pathway / neural crest cell development / COPII vesicle coat / COPII vesicle coating / XBP1(S) activates chaperone genes / endoplasmic reticulum organization / negative regulation of TOR signaling ...vesicle coat / neural crest formation / COPII-coated vesicle cargo loading / vascular endothelial growth factor receptor-2 signaling pathway / neural crest cell development / COPII vesicle coat / COPII vesicle coating / XBP1(S) activates chaperone genes / endoplasmic reticulum organization / negative regulation of TOR signaling / COPII-mediated vesicle transport / positive regulation of protein monoubiquitination / Cul3-RING ubiquitin ligase complex / negative regulation of vascular endothelial growth factor receptor signaling pathway / COPII-coated ER to Golgi transport vesicle / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / endoplasmic reticulum exit site / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / ubiquitin-like ligase-substrate adaptor activity / endoplasmic reticulum to Golgi vesicle-mediated transport / protein-membrane adaptor activity / positive regulation of endothelial cell proliferation / MHC class II antigen presentation / positive regulation of endothelial cell migration / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / apoptotic signaling pathway / intracellular protein transport / response to calcium ion / ER to Golgi transport vesicle membrane / positive regulation of angiogenesis / calcium-dependent protein binding / Signaling by ALK fusions and activated point mutants / protein-macromolecule adaptor activity / cellular response to heat / cytoplasmic vesicle / angiogenesis / endosome / protein dimerization activity / protein heterodimerization activity / intracellular membrane-bounded organelle / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / structural molecule activity / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Takahashi, T. / Suzuki, H. / Kawasaki, M. / Shibata, H. / Wakatsuki, S. / Maki, M. | ||||||
![]() | ![]() Title: Structural Analysis of the Complex between Penta-EF-Hand ALG-2 Protein and Sec31A Peptide Reveals a Novel Target Recognition Mechanism of ALG-2 Authors: Takahashi, T. / Kojima, K. / Zhang, W. / Sasaki, K. / Ito, M. / Suzuki, H. / Kawasaki, M. / Wakatsuki, S. / Takahara, T. / Shibata, H. / Maki, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 88.3 KB | Display | ![]() |
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PDB format | ![]() | 66.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2zndS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20158.492 Da / Num. of mol.: 2 / Fragment: UNP residues 20-191 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1278.458 Da / Num. of mol.: 2 / Fragment: ALG-2 binding site, UNP residues 837-848 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) ![]() #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M Cacodylate, 20% MPD, 0.05M Zinc Acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 21, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28209 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→71 Å / Num. all: 16251 / Num. obs: 16160 / % possible obs: 99.4 % / Redundancy: 10.3 % / Biso Wilson estimate: 36.9 Å2 / Rsym value: 0.08 / Net I/σ(I): 33 |
Reflection shell | Resolution: 2.36→2.421 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 33 / Num. unique all: 16251 / Rsym value: 0.08 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZND Resolution: 2.36→38.094 Å / σ(F): 1.37 / Phase error: 28.13 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.36→38.094 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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