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- PDB-2li9: Metal binding domain of rat beta-amyloid -

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Basic information

Entry
Database: PDB / ID: 2li9
TitleMetal binding domain of rat beta-amyloid
ComponentsAmyloid beta A4 protein
KeywordsCELL ADHESION / Alzheimer's disease / Dimer formation / Zinc binding
Function / homology
Function and homology information


Formyl peptide receptors bind formyl peptides and many other ligands / amyloid-beta complex / ECM proteoglycans / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / Mitochondrial protein degradation / growth cone lamellipodium / Post-translational protein phosphorylation / endosome to plasma membrane transport vesicle / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) ...Formyl peptide receptors bind formyl peptides and many other ligands / amyloid-beta complex / ECM proteoglycans / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / Mitochondrial protein degradation / growth cone lamellipodium / Post-translational protein phosphorylation / endosome to plasma membrane transport vesicle / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to norepinephrine stimulus / TAK1-dependent IKK and NF-kappa-B activation / 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 / ion binding / regulation of epidermal growth factor-activated receptor activity / frizzled binding / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity / heparan sulfate proteoglycan binding / G alpha (q) signalling events / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / G alpha (i) signalling events / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / mating behavior / ciliary rootlet / PTB domain binding / main axon / Golgi-associated vesicle / positive regulation of amyloid fibril formation / neuron remodeling / : / low-density lipoprotein particle receptor binding / suckling behavior / nuclear envelope lumen / dendrite development / COPII-coated ER to Golgi transport vesicle / neuronal dense core vesicle / presynaptic active zone / modulation of excitatory postsynaptic potential / apolipoprotein binding / neuromuscular process controlling balance / regulation of presynapse assembly / transition metal ion binding / negative regulation of long-term synaptic potentiation / regulation of multicellular organism growth / negative regulation of neuron differentiation / intracellular copper ion homeostasis / smooth endoplasmic reticulum / positive regulation of T cell migration / spindle midzone / cellular response to manganese ion / positive regulation of calcium-mediated signaling / positive regulation of chemokine production / clathrin-coated pit / cellular response to cAMP / regulation of peptidyl-tyrosine phosphorylation / forebrain development / 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 / ionotropic glutamate receptor signaling pathway / positive regulation of glycolytic process / cholesterol metabolic process / response to interleukin-1 / positive regulation of mitotic cell cycle / adult locomotory behavior / axonogenesis / extracellular matrix organization / cellular response to nerve growth factor stimulus / positive regulation of peptidyl-threonine phosphorylation / dendritic shaft / learning / positive regulation of interleukin-1 beta production / locomotory behavior / positive regulation of long-term synaptic potentiation / central nervous system development / astrocyte activation / positive regulation of JNK cascade / response to lead ion / synapse organization / microglial cell activation / regulation of long-term neuronal synaptic plasticity
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. / 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 protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing, QM, MM geometry optimization
Model detailsclosest to the average, model 1
AuthorsPolshakov, V. / Istrate, A. / Kozin, S. / Makarov, A.
Citation
Journal: Biophys.J. / Year: 2012
Title: NMR solution structure of rat Abeta(1-16): toward understanding the mechanism of rats' resistance to Alzheimer's disease.
Authors: Istrate, A.N. / Tsvetkov, P.O. / Mantsyzov, A.B. / Kulikova, A.A. / Kozin, S.A. / Makarov, A.A. / Polshakov, V.I.
#1: Journal: MOL.BIOL.(MOSCOW) / Year: 2010
Title: Optimization of the methods for small peptide solution structure determination by NMR spectroscopy.
Authors: Istrate, A.N. / Mantsyzov, A.B. / Kozin, S.A. / Pol'shakov, V.I.
History
DepositionAug 25, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8393
Polymers3,7742
Non-polymers651
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 / 40structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Amyloid beta A4 protein / ABPP / APP / Alzheimer disease amyloid A4 protein homolog / Amyloidogenic glycoprotein / AG


Mass: 1886.998 Da / Num. of mol.: 2 / Fragment: UNP residues 672-687 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P08592
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR solution structure of the dimer of rat beta-Amyloid metal binding domain complexed with zinc ion
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-13C HSQC
1212D DQF-COSY
1322D DQF-COSY
1412D 1H-1H NOESY
1522D 1H-1H NOESY
1622D 1H-1H TOCSY
1712D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
15 mM protein_1, 8 mM Zinc cloride, 20 mM [U-100% 2H] TRIS, 0.1 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
25 mM protein_1, 8 mM Zinc cloride, 20 mM [U-100% 2H] TRIS, 0.1 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5 mMentity_1-11
8 mMZinc cloride-21
20 mMTRIS-3[U-100% 2H]1
0.1 %sodium azide-41
5 mMentity_1-52
8 mMZinc cloride-62
20 mMTRIS-7[U-100% 2H]2
0.1 %sodium azide-82
Sample conditionsIonic strength: 10 / pH: 7.1 / Pressure: ambient / Temperature: 278 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TOPSPINBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SPARKYGoddarddata analysis
AngleSearchV. Polshakovdata analysis
GROMACS3.3.1Van Der Spoel et al.structure solution
GROMACS/CPMDBiswas & Gogoneageometry optimization
ProcheckNMRLaskowski and MacArthurdata analysis
InsightIIAccelrys Software Inc.data analysis
GROMACSVan Der Spoel et al.refinement
GROMACS/CPMDBiswas & Gogonearefinement
RefinementMethod: simulated annealing, QM, MM geometry optimization / Software ordinal: 1 / Details: simulation in explicit water environment
NMR constraintsNOE intraresidue total count: 144 / NOE medium range total count: 30 / NOE sequential total count: 66
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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