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- PDB-2n7r: Structure of the transmembrane domain of human nicastrin in DPC m... -

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Basic information

Entry
Database: PDB / ID: 2n7r
TitleStructure of the transmembrane domain of human nicastrin in DPC micelles
ComponentsNicastrin
KeywordsMEMBRANE PROTEIN / Detergent micelles / gamma-secretase / nicastrin
Function / homology
Function and homology information


amyloid precursor protein biosynthetic process / gamma-secretase complex / aspartic endopeptidase activity, intramembrane cleaving / short-term synaptic potentiation / positive regulation of amyloid precursor protein biosynthetic process / Noncanonical activation of NOTCH3 / positive regulation of endopeptidase activity / Notch receptor processing / central nervous system myelination / membrane protein intracellular domain proteolysis ...amyloid precursor protein biosynthetic process / gamma-secretase complex / aspartic endopeptidase activity, intramembrane cleaving / short-term synaptic potentiation / positive regulation of amyloid precursor protein biosynthetic process / Noncanonical activation of NOTCH3 / positive regulation of endopeptidase activity / Notch receptor processing / central nervous system myelination / membrane protein intracellular domain proteolysis / NOTCH4 Activation and Transmission of Signal to the Nucleus / growth factor receptor binding / Regulated proteolysis of p75NTR / glutamate receptor signaling pathway / amyloid precursor protein metabolic process / regulation of long-term synaptic potentiation / myeloid cell homeostasis / azurophil granule membrane / dopamine receptor signaling pathway / adult behavior / positive regulation of catalytic activity / amyloid precursor protein catabolic process / amyloid-beta formation / membrane protein ectodomain proteolysis / EPH-ephrin mediated repulsion of cells / T cell proliferation / Nuclear signaling by ERBB4 / Notch signaling pathway / NOTCH2 Activation and Transmission of Signal to the Nucleus / cellular response to calcium ion / Degradation of the extracellular matrix / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / cerebellum development / epithelial cell proliferation / NOTCH3 Activation and Transmission of Signal to the Nucleus / sarcolemma / protein processing / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / melanosome / protein-macromolecule adaptor activity / synaptic vesicle / presynaptic membrane / ATPase binding / neuron apoptotic process / learning or memory / early endosome / endosome membrane / Amyloid fiber formation / lysosomal membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / proteolysis / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Nicastrin / Nicastrin, small lobe / Nicastrin / Nicastrin small lobe
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsLi, Y. / Liew, L. / Li, Q. / Kang, C.
CitationJournal: Sci Rep / Year: 2016
Title: Structure of the transmembrane domain of human nicastrin-a component of gamma-secretase
Authors: Li, Y. / Liew, L.S. / Li, Q. / Kang, C.
History
DepositionSep 17, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nicastrin


Theoretical massNumber of molelcules
Total (without water)5,9921
Polymers5,9921
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Nicastrin /


Mass: 5992.000 Da / Num. of mol.: 1 / Fragment: UNP residues 664-709
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q92542

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CA)CB
1413D HN(COCA)CB
1513D HNCO
1613D 1H-15N NOESY
1713D HBHA(CO)NH

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Sample preparation

DetailsContents: 0.8 mM [U-100% 13C; U-100% 15N] transmembrane domain of human nicastrin-1, 20 mM sodium phosphate-2, 200 mM DPC-3, 1 mM DTT-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMtransmembrane domain of human nicastrin-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
200 mMDPC-31
1 mMDTT-41
Sample conditionsIonic strength: 20 / pH: 6.5 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
XPLORE-NIHSchwieters, Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: simulation annealing was conducted. Totally 56 structures were calculated and 20 of them were selected. structures were then energy minimized.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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