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- PDB-2mvx: Atomic-resolution 3D structure of amyloid-beta fibrils: the Osaka... -

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Basic information

Entry
Database: PDB / ID: 2mvx
TitleAtomic-resolution 3D structure of amyloid-beta fibrils: the Osaka mutation
ComponentsAmyloid beta A4 protein
KeywordsPROTEIN FIBRIL / amyloid beta / Osaka mutation / amyloid fibrils
Function / homology
Function and homology information


amyloid-beta complex / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport ...amyloid-beta complex / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / mating behavior / regulation of spontaneous synaptic transmission / ciliary rootlet / Golgi-associated vesicle / PTB domain binding / Lysosome Vesicle Biogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / COPII-coated ER to Golgi transport vesicle / suckling behavior / signaling receptor activator activity / dendrite development / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / presynaptic active zone / positive regulation of protein metabolic process / neuromuscular process controlling balance / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / negative regulation of long-term synaptic potentiation / regulation of presynapse assembly / regulation of multicellular organism growth / transition metal ion binding / intracellular copper ion homeostasis / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / smooth endoplasmic reticulum / Purinergic signaling in leishmaniasis infection / forebrain development / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / protein serine/threonine kinase binding / positive regulation of G2/M transition of mitotic cell cycle / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / response to interleukin-1 / ionotropic glutamate receptor signaling pathway / positive regulation of mitotic cell cycle / cholesterol metabolic process / axonogenesis / positive regulation of calcium-mediated signaling / dendritic shaft / platelet alpha granule lumen / adult locomotory behavior / positive regulation of glycolytic process / central nervous system development / learning / positive regulation of interleukin-1 beta production / trans-Golgi network membrane / positive regulation of long-term synaptic potentiation / endosome lumen / locomotory behavior / astrocyte activation / Post-translational protein phosphorylation / positive regulation of JNK cascade / microglial cell activation / regulation of long-term neuronal synaptic plasticity / serine-type endopeptidase inhibitor activity / synapse organization / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of non-canonical NF-kappaB signal transduction / neuromuscular junction / visual learning / recycling endosome / positive regulation of interleukin-6 production / Golgi lumen / cognition / neuron cellular homeostasis / positive regulation of inflammatory response / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / neuron projection development / G2/M transition of mitotic cell cycle / positive regulation of tumor necrosis factor production / apical part of cell / synaptic vesicle / cell-cell junction / Platelet degranulation
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
Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLID-STATE NMR / torsion angle dynamics
AuthorsSchuetz, A.K. / Vagt, T. / Huber, M. / Ovchinnikova, O.Y. / Cadalbert, R. / Wall, J. / Guentert, P. / Bockmann, A. / Glockshuber, R. / Meier, B.H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Atomic-Resolution Three-Dimensional Structure of Amyloid beta Fibrils Bearing the Osaka Mutation.
Authors: Schutz, A.K. / Vagt, T. / Huber, M. / Ovchinnikova, O.Y. / Cadalbert, R. / Wall, J. / Guntert, P. / Bockmann, A. / Glockshuber, R. / Meier, B.H.
History
DepositionOct 17, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2May 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

Downloads & links

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Assembly

Deposited unit
A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
C: Amyloid beta A4 protein
D: Amyloid beta A4 protein
E: Amyloid beta A4 protein
F: Amyloid beta A4 protein
G: Amyloid beta A4 protein
H: Amyloid beta A4 protein
I: Amyloid beta A4 protein
J: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)42,06710
Polymers42,06710
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)20 / 500target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide
Amyloid beta A4 protein


Mass: 4206.738 Da / Num. of mol.: 10 / Fragment: UNP residues 672-711 / Mutation: E22Delta
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: A4, AD1, APP / Plasmid: pET T7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05067

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NCA
121NCO
132DARR 15 ms
141PAIN 6 ms
153PAIN 6 ms
162DARR 400 ms
175DARR 400 ms
182PAR 8 ms
195PAR 8 ms
1102CHHC 500 us
1115CHHC 500 us
1124PDSD 4 s

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Sample preparation

Details
Solution-IDContentsSolvent system
115 mg/mL [U-100% 13C; U-100% 15N] amyloid beta, 100% H2O100% H2O
215 mg/mL [U-100% 13C] amyloid beta, 100% H2O100% H2O
315 mg/mL [U-100% 13C]/[U-100% 15N] amyloid beta, 100% H2O100% H2O
415 mg/mL [U-100% 2-13C-glucose; U-100% 15N] amyloid beta, 100% H2O100% H2O
515 mg/mL [U-100% 13C; U-100% 15N]/natural abundance amyloid beta, 100% H2O100% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
15 mg/mLamyloid beta-1[U-100% 13C; U-100% 15N]1
15 mg/mLamyloid beta-2[U-100% 13C]2
15 mg/mLamyloid beta-3[U-100% 13C; U-100% 15N]3
15 mg/mLamyloid beta-4[U-100% 2-13C-glucose; U-100% 15N]4
15 mg/mLamyloid beta-5[U-100% 13C; U-100% 15N]/natural abundance5
Sample conditionsIonic strength: 0 / pH: 7 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 850 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.9.6Guntert, Mumenthaler and Wuthrichstructure solution
CcpNMR2.2.2CCPNchemical shift assignment
CcpNMR2.2.2CCPNdata analysis
CcpNMR2.2.2CCPNpeak picking
TALOS+2.1Cornilescu, Delaglio and Baxdihedral angle prediction
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsHydrogen bond constraints total count: 76 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 28 / Protein psi angle constraints total count: 28
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.46 ° / Conformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.0003 Å / Maximum torsion angle constraint violation: 3.4 ° / Maximum upper distance constraint violation: 0.5 Å
NMR ensemble rmsDistance rms dev: 0.01 Å / Distance rms dev error: 0.0001 Å

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