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Yorodumi- PDB-2y2a: Structure of segment KLVFFA from the amyloid-beta peptide (Ab, re... -
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-Basic information
Entry | Database: PDB / ID: 2y2a | ||||||
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Title | Structure of segment KLVFFA from the amyloid-beta peptide (Ab, residues 16-21), alternate polymorph I | ||||||
Components | AMYLOID BETA A4 PROTEIN | ||||||
Keywords | PROTEIN FIBRIL / ALZHEIMER DISEASE | ||||||
Function / homology | Function and homology information regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis ...regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / regulation of Wnt signaling pathway / mating behavior / 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 / presynaptic active zone / nuclear envelope lumen / modulation of excitatory postsynaptic potential / suckling behavior / COPII-coated ER to Golgi transport vesicle / dendrite development / smooth endoplasmic reticulum / regulation of NMDA receptor activity / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / regulation of presynapse assembly / The NLRP3 inflammasome / intracellular copper ion homeostasis / transition metal ion binding / regulation of multicellular organism growth / negative regulation of long-term synaptic potentiation / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / forebrain development / regulation of peptidyl-tyrosine phosphorylation / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / positive regulation of G2/M transition of mitotic cell cycle / ionotropic glutamate receptor signaling pathway / positive regulation of protein metabolic process / neuron projection maintenance / cholesterol metabolic process / extracellular matrix organization / positive regulation of glycolytic process / positive regulation of mitotic cell cycle / response to interleukin-1 / axonogenesis / adult locomotory behavior / trans-Golgi network membrane / dendritic shaft / locomotory behavior / platelet alpha granule lumen / positive regulation of peptidyl-threonine phosphorylation / learning / central nervous system development / positive regulation of interleukin-1 beta production / positive regulation of long-term synaptic potentiation / astrocyte activation / endosome lumen / synapse organization / Post-translational protein phosphorylation / regulation of long-term neuronal synaptic plasticity / positive regulation of JNK cascade / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / visual learning / neuromuscular junction / serine-type endopeptidase inhibitor activity / recycling endosome / cognition / positive regulation of inflammatory response / Golgi lumen / neuron cellular homeostasis / endocytosis / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to amyloid-beta / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / positive regulation of DNA-binding transcription factor activity / G2/M transition of mitotic cell cycle / cell-cell junction / synaptic vesicle / positive regulation of tumor necrosis factor production / regulation of translation Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Colletier, J. / Laganowsky, A. / Sawaya, M.R. / Eisenberg, D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y2a.cif.gz | 9.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y2a.ent.gz | 6.7 KB | Display | PDB format |
PDBx/mmJSON format | 2y2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/2y2a ftp://data.pdbj.org/pub/pdb/validation_reports/y2/2y2a | HTTPS FTP |
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-Related structure data
Related structure data | 2y29C 2y3jC 2y3kC 2y3lC 3ow9C 3pzzC 3q2xC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) HOMO SAPIENS (human) / References: UniProt: P05067 |
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#2: Chemical | ChemComp-ACT / |
#3: 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.71 Å3/Da / Density % sol: 28 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: AB16-21 FORM I CRYSTALS WERE OBTAINED AFTER THE SEGMENT WAS DISSOLVED IN WATER AT 5 MG/ML AND MIXED WITH 0.2 M AMMONIUM ACETATE, 0.1 M BIS-TRIS PH 5.5, 45 % V/V MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
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: 1.9→21.2 Å / Num. obs: 392 / % possible obs: 85 % / Observed criterion σ(I): 3.5 / Redundancy: 3.5 % / Biso Wilson estimate: 19.348 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.9→2.2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.85 / % possible all: 75.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→11.41 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.823 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 16.442 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→11.41 Å /
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