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Yorodumi- PDB-2otk: Structure of Alzheimer Ab peptide in complex with an engineered b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2otk | ||||||
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Title | Structure of Alzheimer Ab peptide in complex with an engineered binding protein | ||||||
Components |
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Keywords | DE NOVO PROTEIN / PEPTIDE BINDING PROTEIN / protein-peptide complex / beta-hairpin / intermolecular beta-sheet | ||||||
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 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 ...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 / 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 / nuclear envelope lumen / suckling behavior / COPII-coated ER to Golgi transport vesicle / dendrite development / 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 / 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 / positive regulation of glycolytic process / ionotropic glutamate receptor signaling pathway / cholesterol metabolic process / response to interleukin-1 / positive regulation of mitotic cell cycle / extracellular matrix organization / axonogenesis / adult locomotory behavior / platelet alpha granule lumen / trans-Golgi network membrane / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-1 beta production / learning / dendritic shaft / positive regulation of long-term synaptic potentiation / central nervous system development / locomotory behavior / endosome lumen / astrocyte activation / positive regulation of JNK cascade / Post-translational protein phosphorylation / microglial cell activation / synapse organization / regulation of long-term neuronal synaptic plasticity / TAK1-dependent IKK and NF-kappa-B activation / serine-type endopeptidase inhibitor activity / visual learning / neuromuscular junction / recycling endosome / cognition / Golgi lumen / positive regulation of inflammatory response / neuron cellular homeostasis / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to amyloid-beta / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of interleukin-6 production / G2/M transition of mitotic cell cycle / positive regulation of tumor necrosis factor production / neuron projection development / cell-cell junction / synaptic vesicle / Platelet degranulation Similarity search - Function | ||||||
Biological species | engineered binding protein (unknown) Homo sapiens (human) | ||||||
Method | SOLUTION NMR / Ab initio simulated annealing | ||||||
Authors | Hoyer, W. / Hard, T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Stabilization of a beta-hairpin in monomeric Alzheimer's amyloid-beta peptide inhibits amyloid formation. Authors: Hoyer, W. / Gronwall, C. / Jonsson, A. / Stahl, S. / Hard, T. #1: Journal: J.BIOTECHNOL. / Year: 2007 Title: Selection and characterization of Affibody ligands binding to Alzheimer amyloid beta peptides Authors: Gronwall, C. / Jonsson, A. / Lindstrom, S. / Gunneriusson, E. / Stahl, S. / Herne, N. | ||||||
History |
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Remark 999 | SEQUENCE Fragments E and F is a dimer of an engineered binding protein, decribed in the Gronwall et ...SEQUENCE Fragments E and F is a dimer of an engineered binding protein, decribed in the Gronwall et al (2007) J. Biotechnol. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2otk.cif.gz | 772.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2otk.ent.gz | 665.8 KB | Display | PDB format |
PDBx/mmJSON format | 2otk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2otk_validation.pdf.gz | 362.6 KB | Display | wwPDB validaton report |
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Full document | 2otk_full_validation.pdf.gz | 718.1 KB | Display | |
Data in XML | 2otk_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 2otk_validation.cif.gz | 65.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/2otk ftp://data.pdbj.org/pub/pdb/validation_reports/ot/2otk | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 4335.852 Da / Num. of mol.: 1 / Fragment: residues 672-711 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05067 |
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#2: Protein | Mass: 7815.620 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) engineered binding protein (unknown) / Production host: Escherichia coli (E. coli) |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: Intermolecular NOEs assigned based on 3D F1 (13C,15N)-filtered, F2 (13C or 15N)-edited NOESY experiments |
-Sample preparation
Details |
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: Ab initio simulated annealing / Software ordinal: 4 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 24 |