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- PDB-8b9r: Molecular structure of Cu(II)-bound amyloid-beta monomer implicat... -

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Basic information

Entry
Database: PDB / ID: 8b9r
TitleMolecular structure of Cu(II)-bound amyloid-beta monomer implicated in inhibition of peptide self-assembly in Alzheimer's disease
ComponentsAmyloid-beta A4 protein
KeywordsMETAL BINDING PROTEIN / Amyloid-beta peptide / Alzheimer's disease / copper ion / paramagnetic NMR / aggregation kinetics
Function / homology
Function and homology information


signaling receptor activator activity / Golgi-associated vesicle / clathrin-coated pit / axonogenesis / central nervous system development / heparin binding / growth cone / perikaryon / early endosome / membrane raft ...signaling receptor activator activity / Golgi-associated vesicle / clathrin-coated pit / axonogenesis / central nervous system development / heparin binding / growth cone / perikaryon / early endosome / membrane raft / signaling receptor binding / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular region / nucleus / plasma membrane
Similarity search - Function
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 ...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 / PH-like domain superfamily
Similarity search - Domain/homology
COPPER (II) ION / Amyloid-beta A4 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsAbelein, A. / Ciofi-Baffoni, S. / Morman, C. / Kumar, R. / Giachetti, A. / Piccioli, M. / Biverstal, H.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
iNEXT1677European Union
CitationJournal: Jacs Au / Year: 2022
Title: Molecular Structure of Cu(II)-Bound Amyloid-beta Monomer Implicated in Inhibition of Peptide Self-Assembly in Alzheimer's Disease.
Authors: Abelein, A. / Ciofi-Baffoni, S. / Morman, C. / Kumar, R. / Giachetti, A. / Piccioli, M. / Biverstal, H.
History
DepositionOct 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 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 A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3992
Polymers4,3361
Non-polymers641
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 5all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Amyloid-beta A4 protein


Mass: 4335.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: B4DM00
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 10 mM no HEPES, 10 % D2 D2O, 100 uM no copper, 75 uM [U-100% 13C; U-100% 15N] amyloid beta, 90% H2O/10% D2O
Details: 75 microM Abeta40 in 10 mM HEPES, 10% D2O, pH 7.2, 100 microM Cu(II)
Label: 13C15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMHEPESno1
10 %D2OD21
100 uMcopperno1
75 uMamyloid beta[U-100% 13C; U-100% 15N]1
Sample conditionsDetails: 75 microM Abeta40 in 10 mM HEPES, 10% D2O, pH 7.2, 100 microM Cu(II)
Ionic strength: 10 mM / Label: condition_1 / pH: 7.2 / Pressure: 1013.25 mbar / Temperature: 281 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE9501TCI cryogenic probe
Bruker AVANCEBrukerAVANCE7002TXO cryogenic probe

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Processing

NMR software
NameVersionDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
NMRFAM-SPARKYLee, Tonelli and Markleychemical shift assignment
NMRFAM-SPARKYLee, Tonelli and Markleypeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 5 / Conformers submitted total number: 5

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