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- PDB-8rq6: Solution NMR structure of Amyloid beta precursor like protein 2 TMD -

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Basic information

Entry
Database: PDB / ID: 8rq6
TitleSolution NMR structure of Amyloid beta precursor like protein 2 TMD
ComponentsAmyloid beta precursor like protein 2
KeywordsMEMBRANE PROTEIN / Transmembrane helix
Function / homology
Function and homology information


platelet alpha granule membrane / transition metal ion binding / axonogenesis / central nervous system development / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / heparin binding / G protein-coupled receptor signaling pathway ...platelet alpha granule membrane / transition metal ion binding / axonogenesis / central nervous system development / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / heparin binding / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / DNA binding / extracellular exosome / identical protein binding / membrane / nucleus / plasma membrane
Similarity search - Function
Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloid precursor protein (APP) E1 domain profile. ...Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / amyloid A4 / Amyloidogenic glycoprotein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Amyloid beta precursor like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMuhle-Goll, C. / Moser, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)263531414/FOR 2290 Germany
CitationJournal: Acs Chem Neurosci / Year: 2024
Title: Substrate Selection Criteria in Regulated Intramembrane Proteolysis.
Authors: Moser, C. / Guschtschin-Schmidt, N. / Silber, M. / Flum, J. / Muhle-Goll, C.
History
DepositionJan 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amyloid beta precursor like protein 2


Theoretical massNumber of molelcules
Total (without water)3,2111
Polymers3,2111
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Amyloid beta precursor like protein 2 / APPH / Amyloid beta (A4) precursor-like protein 2 / Amyloid protein homolog / Amyloid-like protein ...APPH / Amyloid beta (A4) precursor-like protein 2 / Amyloid protein homolog / Amyloid-like protein 2 / APLP-2 / CDEI box-binding protein / CDEBP / Sperm membrane protein YWK-II


Mass: 3211.024 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q06481

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-13C HSQC
131isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution / Contents: 0.5 uM NA APLP2, trifluoroethanol/water / Label: APLP2 / Solvent system: trifluoroethanol/water
SampleConc.: 0.5 uM / Component: APLP2 / Isotopic labeling: NA
Sample conditionsIonic strength: 0 Not defined / Ionic strength err: 0.2 / Label: APLP2 / pH: 6.5 / PH err: 0.2 / Pressure: 1 atm / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: TXI cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CcpNmr Analysis2.4.2CCPNpeak picking
ARIA2.3.2Linge, O'Donoghue and Nilgesstructure calculation
ARIA2.3.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 40

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