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- PDB-2otk: Structure of Alzheimer Ab peptide in complex with an engineered b... -

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Basic information

Entry
Database: PDB / ID: 2otk
TitleStructure of Alzheimer Ab peptide in complex with an engineered binding protein
Components
  • Amyloid beta A4 protein
  • ZAb3 Affibody dimer
KeywordsDE NOVO PROTEIN / PEPTIDE BINDING PROTEIN / protein-peptide complex / beta-hairpin / intermolecular beta-sheet
Function / homology
Function and homology information


amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / microglia development / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / axon midline choice point recognition ...amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / microglia development / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / axon midline choice point recognition / regulation of synapse structure or activity / hippocampal neuron apoptotic process / 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 / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / PTB domain binding / Golgi-associated vesicle / astrocyte projection / Lysosome Vesicle Biogenesis / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / neuron remodeling / nuclear envelope lumen / TRAF6 mediated NF-kB activation / dendrite development / positive regulation of protein metabolic process / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / Advanced glycosylation endproduct receptor signaling / transition metal ion binding / The NLRP3 inflammasome / modulation of excitatory postsynaptic potential / main axon / intracellular copper ion homeostasis / regulation of multicellular organism growth / ECM proteoglycans / response to insulin-like growth factor stimulus / positive regulation of T cell migration / regulation of presynapse assembly / neuronal dense core vesicle / Purinergic signaling in leishmaniasis infection / cellular response to manganese ion / positive regulation of chemokine production / Notch signaling pathway / swimming behavior / neuron projection maintenance / extracellular matrix organization / clathrin-coated pit / positive regulation of mitotic cell cycle / axonogenesis / Mitochondrial protein degradation / positive regulation of calcium-mediated signaling / ionotropic glutamate receptor signaling pathway / platelet alpha granule lumen / astrocyte activation / response to interleukin-1 / cellular response to cAMP / regulation of neuron apoptotic process / cellular response to copper ion / positive regulation of glycolytic process / endosome lumen / trans-Golgi network membrane / positive regulation of interleukin-1 beta production / protein serine/threonine kinase binding / dendritic shaft / positive regulation of long-term synaptic potentiation / learning / central nervous system development / Post-translational protein phosphorylation / adult locomotory behavior / serine-type endopeptidase inhibitor activity / locomotory behavior / microglial cell activation / cellular response to nerve growth factor stimulus / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of non-canonical NF-kappaB signal transduction / synapse organization / visual learning / recycling endosome / positive regulation of interleukin-6 production / positive regulation of JNK cascade / regulation of long-term neuronal synaptic plasticity / Golgi lumen / response to lead ion / cognition / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / endocytosis / neuron projection development / positive regulation of tumor necrosis factor production / positive regulation of inflammatory response / calcium ion transport / Platelet degranulation / regulation of translation / heparin binding / regulation of gene expression
Similarity search - Function
Immunoglobulin FC, subunit C / 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, heparin-binding / Amyloid A4 N-terminal heparin-binding / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) ...Immunoglobulin FC, subunit C / 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, heparin-binding / Amyloid A4 N-terminal heparin-binding / 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, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / PH-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Amyloid-beta precursor protein
Similarity search - Component
Biological speciesengineered binding protein (unknown)
Homo sapiens (human)
MethodSOLUTION NMR / Ab initio simulated annealing
AuthorsHoyer, W. / Hard, T.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Stabilization of a beta-hairpin in monomeric Alzheimer's amyloid-beta peptide inhibits amyloid formation.
Authors: Hoyer, W. / Gronwall, C. / Jonsson, A. / Stahl, S. / Hard, T.
#1: Journal: J.BIOTECHNOL. / Year: 2007
Title: Selection and characterization of Affibody ligands binding to Alzheimer amyloid beta peptides
Authors: Gronwall, C. / Jonsson, A. / Lindstrom, S. / Gunneriusson, E. / Stahl, S. / Herne, N.
History
DepositionFeb 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 4, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Refinement description
Category: diffrn / diffrn_radiation ...diffrn / diffrn_radiation / diffrn_radiation_wavelength / pdbx_nmr_exptl_sample / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_refine / pdbx_nmr_sample_details / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_nmr_exptl_sample_conditions.temperature / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_sample_details.contents
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE Fragments E and F is a dimer of an engineered binding protein, decribed in the Gronwall et ...SEQUENCE Fragments E and F is a dimer of an engineered binding protein, decribed in the Gronwall et al (2007) J. Biotechnol.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Amyloid beta A4 protein
E: ZAb3 Affibody dimer
F: ZAb3 Affibody dimer


Theoretical massNumber of molelcules
Total (without water)19,9673
Polymers19,9673
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2910 Å2
ΔGint-31 kcal/mol
Surface area5890 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 100structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Amyloid beta A4 protein / IgG-binding protein A / Staphylococcal protein A


Mass: 4335.852 Da / Num. of mol.: 1 / Fragment: residues 672-711 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05067
#2: Protein ZAb3 Affibody dimer


Mass: 7815.620 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) engineered binding protein (unknown) / Production host: Escherichia coli (E. coli)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1323D 13C-separated NOESY
1423D 15N-separated NOESY
NMR detailsText: Intermolecular NOEs assigned based on 3D F1 (13C,15N)-filtered, F2 (13C or 15N)-edited NOESY experiments

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Sample preparation

Details
Solution-IDContentsSolvent system
1400 uM [U-100% 13C; U-100% 15N] Abeta peptide, 400 uM ZAb3 dimers, 20 mM Na-phosphate buffer, 90% H2O/10% D2O90% H2O/10% D2O
2400 uM Abeta peptide, 400 uM [U-100% 13C; U-100% 15N] ZAb3 dimers, 20 mM Na-phosphate buffer, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMAbeta peptide[U-100% 13C; U-100% 15N]1
400 uMZAb3 dimersnatural abundance1
400 uMAbeta peptidenatural abundance2
400 uMZAb3 dimers[U-100% 13C; U-100% 15N]2
20 mMNa-phosphate buffernatural abundance1
20 mMNa-phosphate buffernatural abundance2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 mM sodium phophate 7.2ambient 298 K
220 mM sodium phosphate 7.2ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA9001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.15.0Kuszewski et alstructure solution
CcpNmr Analysis1.1Varken et aldata analysis
NMRPipe2.3DeLaglioprocessing
Xplor-NIH2.15.0Kuszewski et alrefinement
RefinementMethod: Ab initio simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 24

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