+Open data
-Basic information
Entry | Database: PDB / ID: 2kr6 | ||||||
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Title | Solution structure of presenilin-1 CTF subunit | ||||||
Components | Presenilin-1 | ||||||
Keywords | HYDROLASE / protease / Alternative splicing / Alzheimer disease / Amyloidosis / Apoptosis / Cell adhesion / Disease mutation / Endoplasmic reticulum / Golgi apparatus / Membrane / Neurodegeneration / Notch signaling pathway / Phosphoprotein / Polymorphism / Transmembrane | ||||||
Function / homology | Function and homology information Cajal-Retzius cell differentiation / positive regulation of L-glutamate import across plasma membrane / positive regulation of coagulation / protein catabolic process at postsynapse / negative regulation of core promoter binding / gamma-secretase complex / aspartic endopeptidase activity, intramembrane cleaving / Noncanonical activation of NOTCH3 / choline transport / Notch receptor processing ...Cajal-Retzius cell differentiation / positive regulation of L-glutamate import across plasma membrane / positive regulation of coagulation / protein catabolic process at postsynapse / negative regulation of core promoter binding / gamma-secretase complex / aspartic endopeptidase activity, intramembrane cleaving / Noncanonical activation of NOTCH3 / choline transport / Notch receptor processing / sequestering of calcium ion / synaptic vesicle targeting / negative regulation of axonogenesis / regulation of resting membrane potential / T cell activation involved in immune response / NOTCH4 Activation and Transmission of Signal to the Nucleus / skin morphogenesis / growth factor receptor binding / neural retina development / dorsal/ventral neural tube patterning / regulation of synaptic vesicle cycle / L-glutamate import across plasma membrane / myeloid dendritic cell differentiation / Regulated proteolysis of p75NTR / regulation of phosphorylation / locomotion / brain morphogenesis / endoplasmic reticulum calcium ion homeostasis / nuclear outer membrane / smooth endoplasmic reticulum calcium ion homeostasis / amyloid precursor protein metabolic process / astrocyte activation involved in immune response / regulation of canonical Wnt signaling pathway / aggresome / embryonic limb morphogenesis / skeletal system morphogenesis / cell fate specification / regulation of postsynapse organization / ciliary rootlet / azurophil granule membrane / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / positive regulation of amyloid fibril formation / positive regulation of receptor recycling / positive regulation of dendritic spine development / mitochondrial transport / positive regulation of catalytic activity / regulation of neuron projection development / heart looping / blood vessel development / amyloid precursor protein catabolic process / cerebral cortex cell migration / smooth endoplasmic reticulum / protein glycosylation / amyloid-beta formation / autophagosome assembly / negative regulation of apoptotic signaling pathway / membrane protein ectodomain proteolysis / EPH-ephrin mediated repulsion of cells / neuron development / rough endoplasmic reticulum / hematopoietic progenitor cell differentiation / somitogenesis / amyloid-beta metabolic process / Nuclear signaling by ERBB4 / Notch signaling pathway / negative regulation of ubiquitin-dependent protein catabolic process / regulation of synaptic transmission, glutamatergic / NOTCH2 Activation and Transmission of Signal to the Nucleus / neuron projection maintenance / Degradation of the extracellular matrix / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / positive regulation of glycolytic process / cerebellum development / post-embryonic development / thymus development / dendritic shaft / negative regulation of protein phosphorylation / epithelial cell proliferation / PDZ domain binding / NOTCH3 Activation and Transmission of Signal to the Nucleus / astrocyte activation / apoptotic signaling pathway / synapse organization / neuron migration / regulation of synaptic plasticity / sarcolemma / neuromuscular junction / calcium channel activity / cell-cell adhesion / protein processing / memory / kinetochore / beta-catenin binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Z disc / neuron cellular homeostasis / positive regulation of protein import into nucleus / cellular response to amyloid-beta Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Doetsch, V. | ||||||
Citation | Journal: To be Published Title: Solution structure of presenilin-1 CTF subunit Authors: Doetsch, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kr6.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2kr6.ent.gz | 892.4 KB | Display | PDB format |
PDBx/mmJSON format | 2kr6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/2kr6 ftp://data.pdbj.org/pub/pdb/validation_reports/kr/2kr6 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 19445.869 Da / Num. of mol.: 1 / Fragment: Presenilin-1 CTF subunit, UNP residues 292-467 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AD3, PS1, PSEN1, PSNL1 / Production host: Escherichia coli (E. coli) References: UniProt: P49768, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 3D HNCA |
-Sample preparation
Details | Contents: 0.5 mM [U-99% 13C; U-99% 15N] ps1ctf-1, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.5 mM / Component: ps1ctf-1 / Isotopic labeling: [U-99% 13C; U-99% 15N] |
Sample conditions | Ionic strength: 20 / pH: 6.8 / Pressure: AMBIENT bar / Temperature: 313 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software | Name: CYANA / Version: 3 / Developer: P.GUNTERT ET AL. / Classification: refinement |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 20 |