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Yorodumi- PDB-2lmq: Structural Model for a 40-residue Beta-Amyloid Fibril with Three-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lmq | ||||||
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Title | Structural Model for a 40-residue Beta-Amyloid Fibril with Three-Fold Symmetry, Negative Stagger | ||||||
Components | Beta-amyloid protein 40 | ||||||
Keywords | PROTEIN FIBRIL / Alzheimer's disease / three-fold 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 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 / : / 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 / 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 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 / 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 / neuron projection development / positive regulation of tumor necrosis factor production / cell-cell junction / synaptic vesicle Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLID-STATE NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Tycko, R. / Paravastu, A. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2008 Title: Molecular structural basis for polymorphism in Alzheimer's beta-amyloid fibrils. Authors: Paravastu, A.K. / Leapman, R.D. / Yau, W.M. / Tycko, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lmq.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2lmq.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 2lmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2lmq_validation.pdf.gz | 603.1 KB | Display | wwPDB validaton report |
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Full document | 2lmq_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 2lmq_validation.xml.gz | 129.8 KB | Display | |
Data in CIF | 2lmq_validation.cif.gz | 200.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/2lmq ftp://data.pdbj.org/pub/pdb/validation_reports/lm/2lmq | HTTPS FTP |
-Related structure data
Related structure data | 2lmnC 2lmoC 2lmpC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-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.: 18 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067 |
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-Experimental details
-Experiment
Experiment | Method: SOLID-STATE NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: selective 13C and 15N beta-amyloid, 10 mM phosphate buffer Solvent system: 10 mM phosphate buffer |
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Sample | Units: mM / Component: beta-amyloid-1 / Isotopic labeling: selective 13C and 15N |
Sample conditions | Ionic strength: 10 / pH: 7.4 / Pressure: ambient / Temperature: 300 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 40 / Conformers submitted total number: 10 |