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Basic information

Entry
Database: PDB / ID: 1nmj
TitleThe Solution Structure of Rat Ab-(1-28) and its Interaction with Zinc: Insights into the Scarity of Amyloid Deposition in Aged Rat Brain
Componentsamyloid beta-peptide from Alzheimer's disease amyloid A4 protein homolog
KeywordsMEMBRANE PROTEIN / Glycoprotein / Amyloid
Function / homology
Function and homology information


amyloid-beta complex / Formyl peptide receptors bind formyl peptides and many other ligands / ECM proteoglycans / growth cone lamellipodium / TAK1-dependent IKK and NF-kappa-B activation / Post-translational protein phosphorylation / TRAF6 mediated NF-kB activation / endosome to plasma membrane transport vesicle / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Advanced glycosylation endproduct receptor signaling ...amyloid-beta complex / Formyl peptide receptors bind formyl peptides and many other ligands / ECM proteoglycans / growth cone lamellipodium / TAK1-dependent IKK and NF-kappa-B activation / Post-translational protein phosphorylation / TRAF6 mediated NF-kB activation / endosome to plasma membrane transport vesicle / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Advanced glycosylation endproduct receptor signaling / cellular response to norepinephrine stimulus / Mitochondrial protein degradation / Platelet degranulation / growth cone filopodium / positive regulation of endothelin production / Lysosome Vesicle Biogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / lipoprotein particle / regulation of amyloid-beta clearance / peptidase activator activity / growth factor receptor binding / astrocyte projection / frizzled binding / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / heparan sulfate proteoglycan binding / regulation of synapse structure or activity / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity / G alpha (q) signalling events / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / G alpha (i) signalling events / regulation of spontaneous synaptic transmission / mating behavior / ciliary rootlet / PTB domain binding / Golgi-associated vesicle / low-density lipoprotein particle receptor binding / main axon / positive regulation of amyloid fibril formation / neuron remodeling / nuclear envelope lumen / suckling behavior / COPII-coated ER to Golgi transport vesicle / dendrite development / neuronal dense core vesicle / presynaptic active zone / modulation of excitatory postsynaptic potential / neuromuscular process controlling balance / apolipoprotein binding / negative regulation of long-term synaptic potentiation / transition metal ion binding / regulation of presynapse assembly / regulation of multicellular organism growth / negative regulation of neuron differentiation / intracellular copper ion homeostasis / spindle midzone / positive regulation of T cell migration / cellular response to manganese ion / smooth endoplasmic reticulum / protein serine/threonine kinase binding / regulation of peptidyl-tyrosine phosphorylation / positive regulation of chemokine production / clathrin-coated pit / forebrain development / cellular response to cAMP / Notch signaling pathway / cellular response to copper ion / neuron projection maintenance / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / positive regulation of calcium-mediated signaling / ionotropic glutamate receptor signaling pathway / positive regulation of glycolytic process / cholesterol metabolic process / extracellular matrix organization / positive regulation of mitotic cell cycle / response to interleukin-1 / axonogenesis / cellular response to nerve growth factor stimulus / adult locomotory behavior / positive regulation of peptidyl-threonine phosphorylation / dendritic shaft / learning / positive regulation of interleukin-1 beta production / positive regulation of long-term synaptic potentiation / central nervous system development / locomotory behavior / astrocyte activation / positive regulation of JNK cascade / response to lead ion / microglial cell activation / synapse organization / regulation of long-term neuronal synaptic plasticity / serine-type endopeptidase inhibitor activity / neuromuscular junction
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 peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus ...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 peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / 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. / 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 precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / 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 protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR
AuthorsHuang, J. / Yao, Y. / Tang, W.X.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2004
Title: The solution structure of rat Abeta-(1-28) and its interaction with zinc ion: insights into the scarcity of amyloid deposition in aged rat brain
Authors: Huang, J. / Yao, Y. / Lin, J. / Ye, Y.H. / Sun, W.Y. / Tang, W.X.
History
DepositionJan 10, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: amyloid beta-peptide from Alzheimer's disease amyloid A4 protein homolog


Theoretical massNumber of molelcules
Total (without water)3,1711
Polymers3,1711
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)1 / -
Representative

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Components

#1: Protein/peptide amyloid beta-peptide from Alzheimer's disease amyloid A4 protein homolog


Mass: 3171.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P08592

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D TOCSY
131DQF-COSY

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Sample preparation

DetailsContents: 2mM rat ab-(1-28) / Solvent system: DMSO
Sample conditionsTemperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR ensembleConformers submitted total number: 1

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