|Entry||Database: PDB / ID: 5buo|
|Title||A receptor molecule|
|Components||Amyloid beta A4 protein|
|Keywords||METAL TRANSPORT / receptor / dimer|
|Function / homology|
Function and homology information
regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / cytoplasmic polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / synaptic assembly at neuromuscular junction / axo-dendritic transport / smooth endoplasmic reticulum calcium ion homeostasis ...regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / cytoplasmic polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / synaptic assembly at neuromuscular junction / axo-dendritic transport / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of Wnt signaling pathway / regulation of spontaneous synaptic transmission / positive regulation of amyloid fibril formation / mating behavior / ciliary rootlet / Golgi-associated vesicle / PTB domain binding / Lysosome Vesicle Biogenesis / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / presynaptic active zone / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / modulation of excitatory postsynaptic potential / nuclear envelope lumen / mRNA polyadenylation / COPII-coated ER to Golgi transport vesicle / suckling behavior / dendrite development / smooth endoplasmic reticulum / regulation of NMDA receptor activity / TRAF6 mediated NF-kB activation / negative regulation of long-term synaptic potentiation / neuromuscular process controlling balance / regulation of presynapse assembly / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / intracellular copper ion homeostasis / transition metal ion binding / regulation of multicellular organism growth / receptor ligand activity / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / Purinergic signaling in leishmaniasis infection / clathrin-coated pit / regulation of peptidyl-tyrosine phosphorylation / forebrain development / positive regulation of chemokine production / Notch signaling pathway / cholesterol metabolic process / astrocyte activation / ionotropic glutamate receptor signaling pathway / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / neuron projection maintenance / axonogenesis / positive regulation of glycolytic process / positive regulation of mitotic cell cycle / response to interleukin-1 / adult locomotory behavior / trans-Golgi network membrane / dendritic shaft / locomotory behavior / extracellular matrix organization / platelet alpha granule lumen / positive regulation of interleukin-1 beta production / positive regulation of peptidyl-threonine phosphorylation / learning / endosome lumen / central nervous system development / positive regulation of long-term synaptic potentiation / synapse organization / Post-translational protein phosphorylation / positive regulation of JNK cascade / visual learning / microglial cell activation / regulation of long-term neuronal synaptic plasticity / TAK1-dependent IKK and NF-kappa-B activation / cognition / neuromuscular junction / serine-type endopeptidase inhibitor activity / recycling endosome / cellular response to amyloid-beta / positive regulation of inflammatory response / neuron cellular homeostasis / positive regulation of interleukin-6 production / Golgi lumen / endocytosis / neuron projection development / positive regulation of non-canonical NF-kappaB signal transduction / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / G2/M transition of mitotic cell cycle / cell-cell junction / positive regulation of DNA-binding transcription factor activity / synaptic vesicle / positive regulation of tumor necrosis factor production / regulation of translation
Similarity search - Function
Amyloid precursor protein, E2 domain / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Beta-amyloid precursor protein C-terminal ...Amyloid precursor protein, E2 domain / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / amyloid A4 / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / PH-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / THIOCYANATE ION / Amyloid-beta precursor protein
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å|
|Authors||Gao, C. / Crespi, G.A.N. / Gorman, M.A. / Nero, T.L. / Parker, M.W. / Miles, L.A.|
|Citation||Journal: To Be Published|
Authors: Miles, L.A.
|Structure viewer||Molecule: |
Downloads & links
A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
|Components on special symmetry positions|
-Protein / Sugars , 2 types, 3 molecules A
Mass: 39199.031 Da / Num. of mol.: 2 / Fragment: UNP Residues 351-691
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: NeuronalNeuron / Cell: Neurons / Gene: APP, A4, AD1 / Organ: Brain / Plasmid: pET11a / Details (production host): AmpR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P05067
|#2: Polysaccharide|| 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose|
Source method: isolated from a genetically manipulated source
-Non-polymers , 8 types, 60 molecules
|#4: Chemical|| ChemComp-CA / ||#5: Chemical||#6: Chemical|| ChemComp-ACT / ||#7: Chemical||#8: Chemical|| ChemComp-SO4 / ||#9: Chemical|| ChemComp-MG / ||#10: Water|| ChemComp-HOH / |
|Sequence details||While chains A and B represent fragments, the authors report that chain A and B are not part of the ...While chains A and B represent fragments, the authors report that chain A and B are not part of the same chain. The start and end of chain A is hard to determine, but likely stretches from 10 to 217 with the sequence YLETPGDENE|
|Experiment||Method: X-RAY DIFFRACTION|
|Crystal||Density Matthews: 1.08 Å3/Da / Density % sol: 65.65 % / Description: buttons and cubes of of 150 x 120 x 10 microns|
|Crystal grow||Temperature: 293 K / Method: vapor diffusion, sitting drop|
Details: PEG3350, ammonium acetate, bis-tris, zinc, thiocyanate
PH range: 5.5-6.5
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.96 Å|
|Detector||Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 11, 2014|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.96 Å / Relative weight: 1|
|Reflection||Resolution: 2.31→37.68 Å / Num. obs: 15277 / % possible obs: 99.5 % / Redundancy: 7.3 % / Biso Wilson estimate: 46.34 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.027 / Net I/σ(I): 15.4|
|Reflection shell||Resolution: 2.31→2.39 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.28 / % possible all: 96.1|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: 3UMI
Resolution: 2.31→37.64 Å / Cor.coef. Fo:Fc: 0.8825 / Cor.coef. Fo:Fc free: 0.8745 / SU R Cruickshank DPI: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.24 / SU Rfree Blow DPI: 0.185 / SU Rfree Cruickshank DPI: 0.185
|Displacement parameters||Biso mean: 63.17 Å2|
|Refine analyze||Luzzati coordinate error obs: 0.353 Å|
|Refinement step||Cycle: LAST / Resolution: 2.31→37.64 Å|
|Refine LS restraints|
|LS refinement shell||Resolution: 2.31→2.47 Å / Total num. of bins used: 8 |
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