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- PDB-1hz3: ALZHEIMER'S DISEASE AMYLOID-BETA PEPTIDE (RESIDUES 10-35) -

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Basic information

Entry
Database: PDB / ID: 1hz3
TitleALZHEIMER'S DISEASE AMYLOID-BETA PEPTIDE (RESIDUES 10-35)
ComponentsA-BETA AMYLOID
KeywordsSUGAR BINDING PROTEIN / collapsed coil / hydrophobic cluster / hydrophobic patch
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
Amyloid-beta precursor protein
Similarity search - Component
MethodSOLUTION NMR / distance geometry, simulated annealing, and restrained molecular dynamics
AuthorsZhang, S. / Iwata, K. / Lachenmann, M.J. / Peng, J.W. / Li, S. / Stimson, E.R. / Lu, Y. / Felix, A.M. / Maggio, J.E. / Lee, J.P.
Citation
Journal: J.Struct.Biol. / Year: 2000
Title: The Alzheimer's peptide a beta adopts a collapsed coil structure in water.
Authors: Zhang, S. / Iwata, K. / Lachenmann, M.J. / Peng, J.W. / Li, S. / Stimson, E.R. / Lu, Y. / Felix, A.M. / Maggio, J.E. / Lee, J.P.
#1: Journal: Biochemistry / Year: 1995
Title: 1H NMR of A-Beta Amyloid Peptide Congeners in Water Solution. Conformational Changes Correlate with Plaque Competence.
Authors: Lee, J.P. / Stimson, E.R. / Ghilardi, J.R. / Mantyh, P.W. / Lu, Y.A. / Felix, A.M. / Llanos, W. / Behbin, A. / Cummings, M. / Van Criekinge, M. / Timms, W. / Maggio, J.E.
#2: Journal: Biophys.J. / Year: 2001
Title: Simulation Study of the Structure and Dynamics of the Alzheimer's Amyloid Peptide Congener in Solution.
Authors: Massi, F. / Peng, J.W. / Lee, J.P. / Straub, J.E.
#3: Journal: Proteins / Year: 2001
Title: Energy Landscape Theory for Alzheimer's Amyloid Beta-Peptide Fibril Elongation
Authors: Massi, F. / Straub, J.E.
History
DepositionJan 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE The peptide residues are numbered 1-26 as they were designated in the distance-geometry ...SEQUENCE The peptide residues are numbered 1-26 as they were designated in the distance-geometry calculation. This corresponds to residues 10-35 of the "Human amyloid peptide Abeta." Abeta is a 40-43 residue peptide derived from the Human amyloid precursor protein (APP) (accession QRHUA4). Residue #10 in Abeta corresponds to residue #681 in APP, and residue #35 in Abeta corresponds to residue #706 in APP.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: A-BETA AMYLOID


Theoretical massNumber of molelcules
Total (without water)2,9071
Polymers2,9071
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)15 / 40structures with the lowest energy
RepresentativeModel #1, 9fewest violations

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Components

#1: Protein/peptide A-BETA AMYLOID / BETA-AMYLOID A4


Mass: 2907.345 Da / Num. of mol.: 1 / Fragment: RESIDUES 10-35 / Source method: obtained synthetically
Details: This sequence is taken from the A-Beta peptide, which occurs naturally in Homo sapiens (human). The peptide was synthesized by Merrifield solid-phase methodology.
References: UniProt: P05067

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
13315N Edited NOESY-HMQC
14313C Edited NOESY
15415N Edited NOESY-HMQC
16413C Edited NOESY
NMR detailsText: Many observed intra-residue NOE-based distance constraints were not included in the structure calculations.

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Sample preparation

Details
Solution-IDContentsSolvent system
1300uM A-Beta(10-35); 90% H2O, 10% D2O90% H2O/10% D2O
2300uM A-Beta(1-40) U-15N; 90% H2O, 10% D2O90% H2O/10% D2O
3300 uM A-Beta(10-35) 2H-Val12, -Leu17, -Val18, -Phe19, -Ile32 and -Leu34; 15N-Phe19, -Val24, -Gly25 and -Gly29; 13C-Val24; 13C-Ala21 Beta Methyl; 13C-Ala30 Beta Methyl; 13C-Met35 Delta Methyl90% H2O/10% D2O
4300 uM A-Beta(10-35) 2H-Val12, -Leu17, -Phe19, -Val24, -Ile31 and -Leu34; 15N-Val 18, -Phe20, -Gly25, -Gly29 and -Gly33; 13C-Val24; 13C-Ala21 Beta Methyl; 13C-Ala30 Beta Methyl; 13C-Met35 Delta Methyl90% H2O/10% D2O
Sample conditionsIonic strength: <1mM / pH: 5.6 / Pressure: ambient / Temperature: 283 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian UNITYPLUSVarianUNITYPLUS7502

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Processing

NMR software
NameVersionDeveloperClassification
VNMR5.3BVarian Associatescollection
DGIIHavel, T.structure solution
Discover3MSI, Inc.refinement
RefinementMethod: distance geometry, simulated annealing, and restrained molecular dynamics
Software ordinal: 1
Details: The structures are based on a total of 84 sequential, 66 medium- (i to i+2 or i+3) and 32 long-range NOE-derived distance constraints.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 15

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