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- PDB-6oc9: S8 phosphorylated beta amyloid 40 fibrils -

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Basic information

Entry
Database: PDB / ID: 6oc9
TitleS8 phosphorylated beta amyloid 40 fibrils
ComponentsAmyloid-beta precursor protein
KeywordsSIGNALING PROTEIN / amyloid fibrils / beta amyloid / phosphorylation / post-translational modification
Function / homology
Function and homology information


amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / regulation of synapse structure or activity ...amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / regulation of synapse structure or activity / axon midline choice point recognition / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / growth factor receptor binding / peptidase activator activity / Golgi-associated vesicle / PTB domain binding / positive regulation of amyloid fibril formation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Lysosome Vesicle Biogenesis / astrocyte projection / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / dendrite development / positive regulation of protein metabolic process / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / modulation of excitatory postsynaptic potential / The NLRP3 inflammasome / transition metal ion binding / main axon / regulation of multicellular organism growth / intracellular copper ion homeostasis / regulation of presynapse assembly / ECM proteoglycans / positive regulation of T cell migration / neuronal dense core vesicle / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / cellular response to manganese ion / Notch signaling pathway / clathrin-coated pit / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / astrocyte activation / ionotropic glutamate receptor signaling pathway / positive regulation of calcium-mediated signaling / positive regulation of mitotic cell cycle / response to interleukin-1 / axonogenesis / protein serine/threonine kinase binding / cellular response to copper ion / platelet alpha granule lumen / cellular response to cAMP / positive regulation of glycolytic process / central nervous system development / positive regulation of interleukin-1 beta production / endosome lumen / dendritic shaft / trans-Golgi network membrane / adult locomotory behavior / positive regulation of long-term synaptic potentiation / learning / positive regulation of JNK cascade / Post-translational protein phosphorylation / locomotory behavior / microglial cell activation / serine-type endopeptidase inhibitor activity / positive regulation of non-canonical NF-kappaB signal transduction / TAK1-dependent IKK and NF-kappa-B activation / regulation of long-term neuronal synaptic plasticity / cellular response to nerve growth factor stimulus / synapse organization / recycling endosome / visual learning / positive regulation of interleukin-6 production / response to lead ion / Golgi lumen / cognition / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endocytosis / cellular response to amyloid-beta / positive regulation of inflammatory response / neuron projection development / positive regulation of tumor necrosis factor production / Platelet degranulation / heparin binding / regulation of translation / regulation of gene expression / early endosome membrane / perikaryon / G alpha (i) signalling events / G alpha (q) signalling events / dendritic spine
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. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site ...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. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / 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
PHOSPHONATE / Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLID-STATE NMR / simulated annealing
AuthorsQiang, W. / Hu, Z.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM125853 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Molecular structure of an N-terminal phosphorylated beta-amyloid fibril.
Authors: Hu, Z.W. / Vugmeyster, L. / Au, D.F. / Ostrovsky, D. / Sun, Y. / Qiang, W.
History
DepositionMar 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amyloid-beta precursor protein
B: Amyloid-beta precursor protein
C: Amyloid-beta precursor protein
D: Amyloid-beta precursor protein
E: Amyloid-beta precursor protein
F: Amyloid-beta precursor protein
G: Amyloid-beta precursor protein
H: Amyloid-beta precursor protein
I: Amyloid-beta precursor protein
J: Amyloid-beta precursor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,15820
Polymers43,35910
Non-polymers80010
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: The assemble restraints were obtained through solid-state NMR distance measurements
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area30030 Å2
ΔGint-203 kcal/mol
Surface area18390 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide
Amyloid-beta precursor protein / APP / ABPP / APPI / Alzheimer disease amyloid protein / Amyloid precursor protein / Amyloid-beta A4 ...APP / ABPP / APPI / Alzheimer disease amyloid protein / Amyloid precursor protein / Amyloid-beta A4 protein / Cerebral vascular amyloid peptide / CVAP / PreA4 / Protease nexin-II / PN-II


Mass: 4335.852 Da / Num. of mol.: 10 / Fragment: residues 616-655 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067
#2: Chemical
ChemComp-2PO / PHOSPHONATE


Mass: 79.980 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: HO3P

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D Spin Diffusion
123anisotropic11D PITHIRDs-CT
133anisotropic11D 13C-31P REDOR
142anisotropic22H relaxation
152anisotropic22H static

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
fibrous protein150 uM 13C, 15N-uniformly labeled E3, G9, V18, F20, D23, S26, K28 beta amyloid peptide, 50 uM 13C, 15N-uniformly labeled A2, F4, D7, Y10, V24, G25 beta amyloid peptide, 50 uM 13C, 15N-uniformly labeled Q15, F19, A21, I31, L34, V36, G37 beta amyloid peptide, 50 uM 13C, 15N-uniformly labeled V12, E22, G29, A30, M35 beta amyloid peptide, 50 uM 13C, 15N-uniformly labeled E11, L17, N27, I32, G33, G38, V39 beta amyloid peptide, 50 uM 13C, 15N-uniformly labeled F19, L34 beta amyloid peptide, 50 uM 13C, 15N-uniformly labeled E3, F4, V24, G25, S26 beta amyloid peptide, 50 uM 13C, 15N-uniformly labeled V12, F20, E22 beta amyloid peptide, 50 uM 13C, 15N-uniformly labeled I31, G33, V39 beta amyloid peptide, water13C, 15N-uniformly labeledwater
fibrous protein250 uM 2H labeled L17, 2H-CD3 beta amyloid peptide, 50 uM 2H labeled F19, 2H-ring-D5 beta amyloid peptide, 50 2H labeled uM L34, 2H-CD3 beta amyloid peptide, 50 uM 2H labeled M35, 2H-CD3 beta amyloid peptide, 50 uM 2H labeled V36, 2H-CD3 beta amyloid peptide, water2H labeledwater
fibrous protein350 uM 13C selective labeled A2-CH3, V12-CO beta amyloid peptide, 50 uM 13C selective labeled V18-CO, A21-CH3 beta amyloid peptide, 50 uM 13C selective labeled V24-CO, A30-CH3 beta amyloid peptide, 50 uM 13C selective labeled G33-CO, V39-Ca beta amyloid peptide, 50 uM 13C selective labeled V36-Ca, G38-CO beta amyloid peptide, 50 uM 13C selective labeled G9-CO beta amyloid peptide, water13C selective labeledwater
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 uME3, G9, V18, F20, D23, S26, K28 beta amyloid peptide13C, 15N-uniformly labeled1
50 uMA2, F4, D7, Y10, V24, G25 beta amyloid peptide13C, 15N-uniformly labeled1
50 uMQ15, F19, A21, I31, L34, V36, G37 beta amyloid peptide13C, 15N-uniformly labeled1
50 uMV12, E22, G29, A30, M35 beta amyloid peptide13C, 15N-uniformly labeled1
50 uME11, L17, N27, I32, G33, G38, V39 beta amyloid peptide13C, 15N-uniformly labeled1
50 uMF19, L34 beta amyloid peptide13C, 15N-uniformly labeled1
50 uME3, F4, V24, G25, S26 beta amyloid peptide13C, 15N-uniformly labeled1
50 uMV12, F20, E22 beta amyloid peptide13C, 15N-uniformly labeled1
50 uMI31, G33, V39 beta amyloid peptide13C, 15N-uniformly labeled1
50 uML17, 2H-CD3 beta amyloid peptide2H labeled2
50 uMF19, 2H-ring-D5 beta amyloid peptide2H labeled2
50 uML34, 2H-CD3 beta amyloid peptide2H labeled2
50 uMM35, 2H-CD3 beta amyloid peptide2H labeled2
50 uMV36, 2H-CD3 beta amyloid peptide2H labeled2
50 uMA2-CH3, V12-CO beta amyloid peptide13C selective labeled3
50 uMV18-CO, A21-CH3 beta amyloid peptide13C selective labeled3
50 uMV24-CO, A30-CH3 beta amyloid peptide13C selective labeled3
50 uMG33-CO, V39-Ca beta amyloid peptide13C selective labeled3
50 uMV36-Ca, G38-CO beta amyloid peptide13C selective labeled3
50 uMG9-CO beta amyloid peptide13C selective labeled3
Sample conditionsIonic strength: 10 mM / Label: condition_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 280 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III7502

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 10

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