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Yorodumi- PDB-2fk3: Structure of the Alzheimer's Amyloid Precursor Protein (APP) Copp... -
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-Basic information
Entry | Database: PDB / ID: 2fk3 | ||||||
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Title | Structure of the Alzheimer's Amyloid Precursor Protein (APP) Copper Binding Domain in 'large unit cell' form | ||||||
Components | Amyloid beta A4 protein precursor | ||||||
Keywords | METAL BINDING PROTEIN / Alpha-Beta Two-layered Sandwich / Non-Crystallographic Symmetry | ||||||
Function / homology | Function and homology information regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of Wnt signaling pathway / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity ...regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of Wnt signaling pathway / regulation of synapse structure or activity / 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 / 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 / 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 / negative regulation of neuron differentiation / intracellular copper ion homeostasis / 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 / response to interleukin-1 / positive regulation of mitotic cell cycle / adult locomotory behavior / axonogenesis / extracellular matrix organization / positive regulation of peptidyl-threonine phosphorylation / platelet alpha granule lumen / trans-Golgi network membrane / dendritic shaft / learning / positive regulation of interleukin-1 beta production / locomotory behavior / positive regulation of long-term synaptic potentiation / central nervous system development / endosome lumen / astrocyte activation / positive regulation of JNK cascade / Post-translational protein phosphorylation / synapse organization / microglial cell activation / regulation of long-term neuronal synaptic plasticity / TAK1-dependent IKK and NF-kappa-B activation / visual learning / serine-type endopeptidase inhibitor activity / neuromuscular junction / recycling endosome / cognition / 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 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / neuron projection development / cell-cell junction / synaptic vesicle Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Kong, G.K.-W. / Parker, M.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structural Studies of the Alzheimer's Amyloid Precursor Protein Copper-binding Domain Reveal How it Binds Copper Ions Authors: Kong, G.K. / Adams, J.J. / Harris, H.H. / Boas, J.F. / Curtain, C.C. / Galatis, D. / Masters, C.L. / Barnham, K.J. / McKinstry, W.J. / Cappai, R. / Parker, M.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fk3.cif.gz | 106.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fk3.ent.gz | 87.7 KB | Display | PDB format |
PDBx/mmJSON format | 2fk3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fk3_validation.pdf.gz | 482 KB | Display | wwPDB validaton report |
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Full document | 2fk3_full_validation.pdf.gz | 490.1 KB | Display | |
Data in XML | 2fk3_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 2fk3_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/2fk3 ftp://data.pdbj.org/pub/pdb/validation_reports/fk/2fk3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
-Components
#1: Protein | Mass: 6848.926 Da / Num. of mol.: 8 / Fragment: Residues 133 to 189 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APP / Plasmid: pPIC-9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P05067 #2: Chemical | ChemComp-CU / #3: 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: 2.34 Å3/Da / Density % sol: 47.46 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 0.1 M MES pH 5.4 - 5.6, 0.4 M NaCOOH, 10 - 15 % (w/v) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.3786 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 13, 2003 / Details: Bent cylindrical Si-mirror (Rh coated) |
Radiation | Monochromator: Diamond (111) double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3786 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 20578 / Num. obs: 20981 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 11.4 % / Biso Wilson estimate: 34.1 Å2 / Rsym value: 0.072 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 6 % / Mean I/σ(I) obs: 9.3 / Rsym value: 0.143 / % possible all: 86.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→19.88 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1444276.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.6865 Å2 / ksol: 0.369541 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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