[English] 日本語
Yorodumi- PDB-2lp1: The solution NMR structure of the transmembrane C-terminal domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lp1 | ||||||
---|---|---|---|---|---|---|---|
Title | The solution NMR structure of the transmembrane C-terminal domain of the amyloid precursor protein (C99) | ||||||
Components | C99 | ||||||
Keywords | MEMBRANE PROTEIN / AMYLOID PRECURSOR PROTEIN C-TERMINAL FRAGMENT / ALZHEIMER'S DISEASE / AMYLOID-BETA PRECURSOR / TRANSMEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis ...regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / regulation of Wnt signaling pathway / mating behavior / 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 / presynaptic active zone / nuclear envelope lumen / modulation of excitatory postsynaptic potential / suckling behavior / COPII-coated ER to Golgi transport vesicle / dendrite development / smooth endoplasmic reticulum / regulation of NMDA receptor activity / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / regulation of presynapse assembly / The NLRP3 inflammasome / intracellular copper ion homeostasis / transition metal ion binding / regulation of multicellular organism growth / negative regulation of long-term synaptic potentiation / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / forebrain development / regulation of peptidyl-tyrosine phosphorylation / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / positive regulation of G2/M transition of mitotic cell cycle / ionotropic glutamate receptor signaling pathway / positive regulation of protein metabolic process / neuron projection maintenance / cholesterol metabolic process / extracellular matrix organization / positive regulation of glycolytic process / positive regulation of mitotic cell cycle / response to interleukin-1 / axonogenesis / adult locomotory behavior / trans-Golgi network membrane / dendritic shaft / locomotory behavior / platelet alpha granule lumen / positive regulation of peptidyl-threonine phosphorylation / learning / central nervous system development / positive regulation of interleukin-1 beta production / positive regulation of long-term synaptic potentiation / astrocyte activation / endosome lumen / synapse organization / Post-translational protein phosphorylation / regulation of long-term neuronal synaptic plasticity / positive regulation of JNK cascade / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / visual learning / neuromuscular junction / serine-type endopeptidase inhibitor activity / recycling endosome / cognition / positive regulation of inflammatory response / Golgi lumen / neuron cellular homeostasis / endocytosis / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to amyloid-beta / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / positive regulation of DNA-binding transcription factor activity / G2/M transition of mitotic cell cycle / cell-cell junction / synaptic vesicle / positive regulation of tumor necrosis factor production / regulation of translation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / molecular dynamics, simulated annealing | ||||||
Model details | closest to the average, model 5 | ||||||
Authors | Barrett, P.J. / Song, Y. / Van Horn, W.D. / Hustedt, E.J. / Schafer, J.M. / Hadziselimovic, A. / Beel, A.J. / Sanders, C.R. | ||||||
Citation | Journal: Science / Year: 2012 Title: The amyloid precursor protein has a flexible transmembrane domain and binds cholesterol. Authors: Barrett, P.J. / Song, Y. / Van Horn, W.D. / Hustedt, E.J. / Schafer, J.M. / Hadziselimovic, A. / Beel, A.J. / Sanders, C.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2lp1.cif.gz | 443.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2lp1.ent.gz | 362.1 KB | Display | PDB format |
PDBx/mmJSON format | 2lp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/2lp1 ftp://data.pdbj.org/pub/pdb/validation_reports/lp/2lp1 | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 13801.766 Da / Num. of mol.: 1 / Fragment: UNP residues 683-728 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: A4, AD1, APP / Production host: Escherichia coli (E. coli) / References: UniProt: P05067 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||||||||||||||
NMR details | Text: All 2D and 3D experiments were TROSY based. For the RDC data collection, the TROSY/Semi-TROSY method was used. |
-Sample preparation
Details | Contents: 10 % lyso myristoyl phosphatidylglycerol, 10 % [U-2H] D2O, 100 mM imidazole, 250 uM [U-100% 15N] APP_C99, 1 mM EDTA, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sample conditions | pH: 6.5 / Pressure: ambient / Temperature: 318 K |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: molecular dynamics, simulated annealing / Software ordinal: 1 Details: RESTRAINED MOLECULAR DYNAMICS WITH SIMULATED ANNEALING, FOLLOWED BY POWELL ENERGY MINIMIZATION | ||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 65 / NOE intraresidue total count: 0 / NOE long range total count: 0 / NOE medium range total count: 22 / NOE sequential total count: 43 / Hydrogen bond constraints total count: 13 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 33 / Protein psi angle constraints total count: 32 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 0.351 ° Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 30 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 0.56 ° / Maximum upper distance constraint violation: 0 Å / Torsion angle constraint violation method: NIH Xplor | ||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0 Å / Distance rms dev error: 0 Å |