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- PDB-6ti5: A New Structural Model of Abeta(1-40) Fibrils -

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Basic information

Entry
Database: PDB / ID: 6ti5
TitleA New Structural Model of Abeta(1-40) Fibrils
ComponentsAmyloid-beta precursor protein
KeywordsPROTEIN FIBRIL / amyloid beta peptides / Alzheimer's disease / supramolecular assembly
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 / signaling receptor activator activity / Advanced glycosylation endproduct receptor signaling / 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 / ECM proteoglycans / regulation of presynapse assembly / 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 / axonogenesis / positive regulation of calcium-mediated signaling / positive regulation of mitotic cell cycle / response to interleukin-1 / 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 / adult locomotory behavior / positive regulation of interleukin-1 beta production / endosome lumen / dendritic shaft / trans-Golgi network membrane / positive regulation of long-term synaptic potentiation / TAK1-dependent IKK and NF-kappa-B activation / 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 / regulation of long-term neuronal synaptic plasticity / synapse organization / cellular response to nerve growth factor stimulus / recycling endosome / visual learning / positive regulation of interleukin-6 production / response to lead ion / Golgi lumen / cognition / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / 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
Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLID-STATE NMR / molecular dynamics
AuthorsBertini, I. / Gonnelli, L. / Luchinat, C. / Mao, J. / Nesi, A.
Citation
Journal: Chem.Commun.(Camb.) / Year: 2020
Title: Mixing A beta (1-40) and A beta (1-42) peptides generates unique amyloid fibrils.
Authors: Cerofolini, L. / Ravera, E. / Bologna, S. / Wiglenda, T. / Boddrich, A. / Purfurst, B. / Benilova, I. / Korsak, M. / Gallo, G. / Rizzo, D. / Gonnelli, L. / Fragai, M. / De Strooper, B. / ...Authors: Cerofolini, L. / Ravera, E. / Bologna, S. / Wiglenda, T. / Boddrich, A. / Purfurst, B. / Benilova, I. / Korsak, M. / Gallo, G. / Rizzo, D. / Gonnelli, L. / Fragai, M. / De Strooper, B. / Wanker, E.E. / Luchinat, C.
#1: Journal: J. Am. Chem. Soc. / Year: 2011
Title: A new structural model of Abeta40 fibrils.
Authors: Bertini, I. / Gonnelli, L. / Luchinat, C. / Mao, J. / Nesi, A.
History
DepositionNov 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
K: Amyloid-beta precursor protein
L: Amyloid-beta precursor protein
M: Amyloid-beta precursor protein
N: Amyloid-beta precursor protein
O: Amyloid-beta precursor protein
P: Amyloid-beta precursor protein


Theoretical massNumber of molelcules
Total (without water)69,37416
Polymers69,37416
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area44500 Å2
ΔGint-275 kcal/mol
Surface area18270 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 200Top 4 Structures From HADDOCK
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.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APP, A4, AD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P05067

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic22D 15N-13C NCA
121anisotropic22D 15N-13C NCO
131anisotropic23D NCACX
141anisotropic23D NCOCX
151anisotropic23D CANCO
161anisotropic22D 13C-13C DARR (<100 ms)
171anisotropic22D 15N-13C PAIN
181anisotropic12D 13C-13C DARR/PDSD (>100 ms)
191anisotropic22D 13C-13C PAR (10-15 ms)

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Sample preparation

DetailsType: fiber
Contents: 100 uM [U-100% 13C; U-100% 15N] Amyloid beta peptide 1-40, 50 mM ammonium acetate, H2O
Details: The fibrils were grown in ammonium acetate buffer and then washed with fresh, cold ultrapure water (Millipore) three times.
Label: 13C 15N Ab(1-40) / Solvent system: H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 uMAmyloid beta peptide 1-40[U-100% 13C; U-100% 15N]4
50 mMammonium acetatenatural abundance4
Sample conditionsIonic strength: 0 Not defined / Label: condition_1 / pH: 8.5 / Pressure: 1 atm / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II7001
Bruker AVANCE IIIBrukerAVANCE III8502

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
SparkyGoddardchemical shift assignment
HADDOCKBonvinstructure calculation
RefinementMethod: molecular dynamics / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Top 4 Structures From HADDOCK / Conformers calculated total number: 200 / Conformers submitted total number: 4

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