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- PDB-2kr6: Solution structure of presenilin-1 CTF subunit -

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Basic information

Entry
Database: PDB / ID: 2kr6
TitleSolution structure of presenilin-1 CTF subunit
ComponentsPresenilin-1
KeywordsHYDROLASE / 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 / negative regulation of core promoter binding / gamma-secretase complex / aspartic endopeptidase activity, intramembrane cleaving / Noncanonical activation of NOTCH3 / protein catabolic process at postsynapse / TGFBR3 PTM regulation / sequestering of calcium ion / Notch receptor processing ...Cajal-Retzius cell differentiation / positive regulation of L-glutamate import across plasma membrane / negative regulation of core promoter binding / gamma-secretase complex / aspartic endopeptidase activity, intramembrane cleaving / Noncanonical activation of NOTCH3 / protein catabolic process at postsynapse / TGFBR3 PTM regulation / sequestering of calcium ion / Notch receptor processing / synaptic vesicle targeting / positive regulation of coagulation / negative regulation of axonogenesis / growth factor receptor binding / T cell activation involved in immune response / skin morphogenesis / choline transport / NOTCH4 Activation and Transmission of Signal to the Nucleus / dorsal/ventral neural tube patterning / neural retina development / regulation of resting membrane potential / myeloid dendritic cell differentiation / L-glutamate import across plasma membrane / Regulated proteolysis of p75NTR / regulation of phosphorylation / locomotion / brain morphogenesis / endoplasmic reticulum calcium ion homeostasis / nuclear outer membrane / amyloid precursor protein metabolic process / regulation of synaptic vesicle cycle / smooth endoplasmic reticulum calcium ion homeostasis / embryonic limb morphogenesis / regulation of postsynapse organization / astrocyte activation involved in immune response / cell fate specification / regulation of canonical Wnt signaling pathway / skeletal system morphogenesis / aggresome / azurophil granule membrane / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ciliary rootlet / positive regulation of dendritic spine development / positive regulation of amyloid fibril formation / positive regulation of receptor recycling / regulation of neuron projection development / protein glycosylation / blood vessel development / mitochondrial transport / amyloid precursor protein catabolic process / heart looping / cerebral cortex cell migration / amyloid-beta formation / membrane protein ectodomain proteolysis / negative regulation of apoptotic signaling pathway / autophagosome assembly / EPH-ephrin mediated repulsion of cells / negative regulation of ubiquitin-dependent protein catabolic process / neuron development / somitogenesis / smooth endoplasmic reticulum / hematopoietic progenitor cell differentiation / Nuclear signaling by ERBB4 / calcium ion homeostasis / regulation of synaptic transmission, glutamatergic / rough endoplasmic reticulum / Notch signaling pathway / Degradation of the extracellular matrix / neuron projection maintenance / NOTCH2 Activation and Transmission of Signal to the Nucleus / cerebellum development / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / dendritic shaft / thymus development / positive regulation of glycolytic process / epithelial cell proliferation / post-embryonic development / PDZ domain binding / astrocyte activation / NOTCH3 Activation and Transmission of Signal to the Nucleus / apoptotic signaling pathway / synapse organization / neuromuscular junction / sarcolemma / protein processing / beta-catenin binding / cell-cell adhesion / regulation of synaptic plasticity / kinetochore / calcium channel activity / memory / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / positive regulation of protein import into nucleus / neuron cellular homeostasis / cellular response to amyloid-beta / neuron migration / positive regulation of tumor necrosis factor production / cell junction
Similarity search - Function
Presenilin / Peptidase A22A, presenilin 1 / Peptidase A22A, presenilin / Presenilin, C-terminal / Presenilin / Presenilin/signal peptide peptidase / Presenilin, signal peptide peptidase, family / Cyclin A; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsDoetsch, V.
CitationJournal: To be Published
Title: Solution structure of presenilin-1 CTF subunit
Authors: Doetsch, V.
History
DepositionDec 4, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Presenilin-1


Theoretical massNumber of molelcules
Total (without water)19,4461
Polymers19,4461
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Presenilin-1 / PS-1 / Protein S182


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D HNCA

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Sample preparation

DetailsContents: 0.5 mM [U-99% 13C; U-99% 15N] ps1ctf-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: ps1ctf-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 20 / pH: 6.8 / Pressure: AMBIENT bar / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE8003
Bruker AvanceBrukerAVANCE9504

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Processing

NMR softwareName: CYANA / Version: 3 / Developer: P.GUNTERT ET AL. / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 20

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