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- PDB-5lfy: Zinc bound dimer of the fragment of human amyloid-beta peptide wi... -

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Basic information

Entry
Database: PDB / ID: 5lfy
TitleZinc bound dimer of the fragment of human amyloid-beta peptide with Alzheimer's disease pathogenic Taiwanese mutation D7H
ComponentsAmyloid beta A4 protein
KeywordsSTRUCTURAL PROTEIN / Alzheimer's disease / amyloid-beta peptide / zinc complex / zinc-bound dimer
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 / regulation of synapse structure or activity / axo-dendritic transport / regulation of Wnt signaling pathway ...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 / regulation of synapse structure or activity / axo-dendritic transport / regulation of Wnt signaling pathway / 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 / Lysosome Vesicle Biogenesis / positive regulation of amyloid fibril formation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / astrocyte projection / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / positive regulation of protein metabolic process / dendrite development / TRAF6 mediated NF-kB activation / modulation of excitatory postsynaptic potential / Advanced glycosylation endproduct receptor signaling / signaling receptor activator activity / The NLRP3 inflammasome / negative regulation of long-term synaptic potentiation / main axon / transition metal ion binding / 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 / clathrin-coated pit / Notch signaling pathway / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / astrocyte activation / ionotropic glutamate receptor signaling pathway / axonogenesis / response to interleukin-1 / positive regulation of mitotic cell cycle / positive regulation of calcium-mediated signaling / protein serine/threonine kinase binding / cellular response to copper ion / platelet alpha granule lumen / cellular response to cAMP / positive regulation of glycolytic process / adult locomotory behavior / central nervous system development / positive regulation of long-term synaptic potentiation / positive regulation of interleukin-1 beta production / trans-Golgi network membrane / endosome lumen / dendritic shaft / 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 / regulation of long-term neuronal synaptic plasticity / positive regulation of non-canonical NF-kappaB signal transduction / synapse organization / cellular response to nerve growth factor stimulus / visual learning / recycling endosome / response to lead ion / positive regulation of interleukin-6 production / Golgi lumen / cognition / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of inflammatory response / cellular response to amyloid-beta / neuron projection development / positive regulation of tumor necrosis factor production / Platelet degranulation / heparin binding / regulation of gene expression / regulation of translation / early endosome membrane / G alpha (i) signalling events / perikaryon / 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 A4 protein / Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsPolshakov, V.I. / Mantsyzov, A.B. / Kozin, S.A.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation14-24-00100 Russian Federation
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: A Binuclear Zinc Interaction Fold Discovered in the Homodimer of Alzheimer's Amyloid-beta Fragment with Taiwanese Mutation D7H.
Authors: Polshakov, V.I. / Mantsyzov, A.B. / Kozin, S.A. / Adzhubei, A.A. / Zhokhov, S.S. / van Beek, W. / Kulikova, A.A. / Indeykina, M.I. / Mitkevich, V.A. / Makarov, A.A.
History
DepositionJul 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_spectrometer / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,5694
Polymers2,4392
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area820 Å2
ΔGint-76 kcal/mol
Surface area2190 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Amyloid beta A4 protein


Mass: 1219.267 Da / Num. of mol.: 2 / Fragment: UNP residues 17-26 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: L7XE61, UniProt: P05067*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D DQF-COSY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H NOESY
1112isotropic12D 1H-1H NOESY
141isotropic12D 1H-15N HSQC
151isotropic12D 1H-13C HSQC aliphatic
161isotropic12D 1H-13C HSQC aromatic
172isotropic12D 1H-13C HSQC aliphatic
182isotropic12D 1H-1H ROESY
192isotropic12D DQF-COSY
1102isotropic12D DOSY
1123isotropic12D 1H-15N HMBC
1133isotropic12D 13C-edited,13C-filtered NOESY
1143isotropic12D 1H-15N HMBC-NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.4 mM D7H_Abeta(1-10), 2.8 mM ZnCl2, 10 mM [U-99% 2D] bis-Tris-d19, 90% H2O/10% D2OD7HAbeta10_H2O90% H2O/10% D2O
solution21.4 mM D7H_Abeta(1-10), 2.8 mM ZnCl2, 10 mM [U-99% 2D] bis-Tris-d19, 100% D2OD7HAbeta10_D2O100% D2O
solution30.8 mM D7H_Abeta(1-10), 0.8 mM [U-99% 13C,15N]-(D1,3); [U-99% 15N]-(H6,H7) D7H_Abeta(1-10), 1.7 mM ZnCl2, 10 mM [U-99% 2D] bis-Tris-d19, 100% D2OD7HAbeta10_labeled100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.4 mMD7H_Abeta(1-10)natural abundance1
2.8 mMZnCl2natural abundance1
10 mMbis-Tris-d19[U-99% 2D]1
1.4 mMD7H_Abeta(1-10)natural abundance2
2.8 mMZnCl2natural abundance2
10 mMbis-Tris-d19[U-99% 2D]2
0.8 mMD7H_Abeta(1-10)natural abundance3
0.8 mMD7H_Abeta(1-10)_label[U-99% 13C,15N]-(D1,3); [U-99% 15N]-(H6,H7)3
1.7 mMZnCl2natural abundance3
10 mMbis-Tris-d19[U-99% 2D]3
Sample conditionsIonic strength: 3 mM / Label: conditions_1 / pH: 7 / PH err: 0.02 / Pressure: 1 atm / Temperature: 278 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
AnglesearchPolshakovdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
PROCHECK / PROCHECK-NMRLaskowski and MacArthurdata analysis
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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