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- PDB-2y29: Structure of segment KLVFFA from the amyloid-beta peptide (Ab, re... -
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Basic information
Entry | Database: PDB / ID: 2y29 | ||||||
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Title | Structure of segment KLVFFA from the amyloid-beta peptide (Ab, residues 16-21), alternate polymorph III | ||||||
![]() | AMYLOID BETA A4 PROTEIN | ||||||
![]() | PROTEIN FIBRIL / ALZHEIMER DISEASE | ||||||
Function / homology | ![]() regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity ...regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / mating behavior / NMDA selective glutamate receptor signaling pathway / ciliary rootlet / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / positive regulation of amyloid fibril formation / neuron remodeling / : / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / suckling behavior / nuclear envelope lumen / dendrite development / COPII-coated ER to Golgi transport vesicle / presynaptic active zone / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / The NLRP3 inflammasome / regulation of presynapse assembly / transition metal ion binding / negative regulation of long-term synaptic potentiation / regulation of multicellular organism growth / intracellular copper ion homeostasis / negative regulation of neuron differentiation / ECM proteoglycans / smooth endoplasmic reticulum / positive regulation of T cell migration / spindle midzone / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / protein serine/threonine kinase binding / positive regulation of chemokine production / clathrin-coated pit / regulation of peptidyl-tyrosine phosphorylation / forebrain development / Notch signaling pathway / Mitochondrial protein degradation / neuron projection maintenance / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / ionotropic glutamate receptor signaling pathway / positive regulation of glycolytic process / cholesterol metabolic process / positive regulation of mitotic cell cycle / response to interleukin-1 / adult locomotory behavior / extracellular matrix organization / axonogenesis / platelet alpha granule lumen / trans-Golgi network membrane / positive regulation of peptidyl-threonine phosphorylation / dendritic shaft / learning / positive regulation of interleukin-1 beta production / positive regulation of long-term synaptic potentiation / locomotory behavior / central nervous system development / endosome lumen / astrocyte activation / positive regulation of JNK cascade / Post-translational protein phosphorylation / synapse organization / regulation of long-term neuronal synaptic plasticity / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / visual learning / serine-type endopeptidase inhibitor activity / neuromuscular junction / recycling endosome / cognition / neuron cellular homeostasis / Golgi lumen / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / endocytosis / cellular response to amyloid-beta / G2/M transition of mitotic cell cycle / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / neuron projection development / cell-cell junction / synaptic vesicle Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Colletier, J. / Laganowsky, A. / Sawaya, M.R. / Eisenberg, D. | ||||||
![]() | ![]() Title: Molecular Basis for Amyloid-{Beta} Polymorphism. Authors: Colletier, J. / Laganowsky, A. / Landau, M. / Zhao, M. / Soriaga, A.B. / Goldschmidt, L. / Flot, D. / Cascio, D. / Sawaya, M.R. / Eisenberg, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 9.2 KB | Display | ![]() |
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PDB format | ![]() | 6.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 401.5 KB | Display | ![]() |
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Full document | ![]() | 401.4 KB | Display | |
Data in XML | ![]() | 2.3 KB | Display | |
Data in CIF | ![]() | 2.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y2aC ![]() 2y3jC ![]() 2y3kC ![]() 2y3lC ![]() 3ow9C ![]() 3pzzC ![]() 3q2xC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 724.909 Da / Num. of mol.: 1 / Fragment: SEGMENT KLVFFA, RESIDUES 687-692 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#2: Water | ChemComp-HOH / |
Sequence details | IN VIVO AMYLOID BETA PEPTIDE (AB) IS A PROTEOLYTIC PRODUCT OF THE AMYLOID PRECURSOR PROTEIN (APP). ...IN VIVO AMYLOID BETA PEPTIDE (AB) IS A PROTEOLYTI |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.73 Å3/Da / Density % sol: 29 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: AB16-21 FORM III CRYSTALS WERE OBTAINED AFTER THE SEGMENT WAS DISSOLVED IN WATER AT 5 MG/ML AND MIXED WITH 0.2M AMMONIUM ACETATE, 0.1 M TRIS BUFFER PH 8.5 AND 30% ISOPROPANOL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 266 / % possible obs: 94.3 % / Observed criterion σ(I): 3 / Redundancy: 3.9 % / Biso Wilson estimate: 34.134 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.19 / % possible all: 89.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.654 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å /
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