[English] 日本語
Yorodumi- PDB-3dxd: Crystal structure of the intracellular domain of human APP (T668E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dxd | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the intracellular domain of human APP (T668E mutant) in complex with Fe65-PTB2 | ||||||
Components |
| ||||||
Keywords | PROTEIN BINDING / Alzheimer's disease / APP / AICD / Fe65 / PTB domain / Alzheimer disease / Amyloid / Apoptosis / Cell adhesion / Coated pit / Disease mutation / Endocytosis / Glycoprotein / Heparin-binding / Iron / Membrane / Metal-binding / Notch signaling pathway / Phosphoprotein / Protease inhibitor / Proteoglycan / Serine protease inhibitor / Transmembrane | ||||||
Function / homology | Function and homology information negative regulation of cell cycle G1/S phase transition / regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction ...negative regulation of cell cycle G1/S phase transition / regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / proline-rich region binding / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / mating behavior / NMDA selective glutamate receptor signaling pathway / ciliary rootlet / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / positive regulation of amyloid fibril formation / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / low-density lipoprotein particle receptor binding / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / : / suckling behavior / nuclear envelope lumen / dendrite development / COPII-coated ER to Golgi transport vesicle / presynaptic active zone / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / The NLRP3 inflammasome / regulation of presynapse assembly / transition metal ion binding / negative regulation of long-term synaptic potentiation / regulation of multicellular organism growth / intracellular copper ion homeostasis / negative regulation of neuron differentiation / smooth muscle contraction / ECM proteoglycans / smooth endoplasmic reticulum / positive regulation of T cell migration / spindle midzone / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / protein serine/threonine kinase binding / positive regulation of chemokine production / clathrin-coated pit / regulation of peptidyl-tyrosine phosphorylation / forebrain development / Notch signaling pathway / Mitochondrial protein degradation / neuron projection maintenance / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / ionotropic glutamate receptor signaling pathway / positive regulation of glycolytic process / cholesterol metabolic process / positive regulation of mitotic cell cycle / response to interleukin-1 / adult locomotory behavior / extracellular matrix organization / axonogenesis / platelet alpha granule lumen / trans-Golgi network membrane / positive regulation of peptidyl-threonine phosphorylation / dendritic shaft / learning / positive regulation of interleukin-1 beta production / positive regulation of long-term synaptic potentiation / locomotory behavior / central nervous system development / endosome lumen / astrocyte activation / positive regulation of protein secretion / positive regulation of JNK cascade / Post-translational protein phosphorylation / synapse organization / regulation of long-term neuronal synaptic plasticity / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / visual learning / serine-type endopeptidase inhibitor activity / neuromuscular junction / recycling endosome / cognition / positive regulation of neuron projection development / neuron cellular homeostasis / Golgi lumen / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / endocytosis / cellular response to amyloid-beta / G2/M transition of mitotic cell cycle Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Radzimanowski, J. / Sinning, I. / Wild, K. | ||||||
Citation | Journal: Embo Rep. / Year: 2008 Title: Structure of the intracellular domain of the amyloid precursor protein in complex with Fe65-PTB2. Authors: Radzimanowski, J. / Simon, B. / Sattler, M. / Beyreuther, K. / Sinning, I. / Wild, K. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Overproduction, purification, crystallization and preliminary X-ray analysis of human Fe65-PTB2 in complex with the amyloid precursor protein intracellular domain Authors: Radzimanowski, R. / Beyreuther, K. / Sinning, I. / Wild, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3dxd.cif.gz | 75.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3dxd.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 3dxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dxd_validation.pdf.gz | 456.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3dxd_full_validation.pdf.gz | 461.5 KB | Display | |
Data in XML | 3dxd_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 3dxd_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/3dxd ftp://data.pdbj.org/pub/pdb/validation_reports/dx/3dxd | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | THE ASYMMETRIC UNIT CONTAINS TWO COPIES OF A PROTEIN PROTEIN COMPLEX (ONE BIOMOLECULE 1 BINDS ONE BIOMOLECULE 2). |
-Components
#1: Protein | Mass: 15459.690 Da / Num. of mol.: 2 / Fragment: PTB2 domain, UNP residues 534-667 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APBB1, FE65, RIR / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: O00213 #2: Protein/peptide | Mass: 4123.515 Da / Num. of mol.: 2 / Fragment: APP intracellular domain, UNP residues 739-770 / Mutation: T668E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APP, A4, AD1 / Plasmid: pETtrx_1b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P05067 #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.72 Å3/Da / Density % sol: 66.97 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.6 Details: 3.2 M NaCl, 0.1 M sodium acetate , pH 4.6, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 19, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→60 Å / Num. obs: 28638 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 30.3 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3.9 / % possible all: 97.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.2→37.69 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.87 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 95.01 Å2 / Biso mean: 50.925 Å2 / Biso min: 21.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→37.69 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
|