+Open data
-Basic information
Entry | Database: PDB / ID: 1hz3 | ||||||
---|---|---|---|---|---|---|---|
Title | ALZHEIMER'S DISEASE AMYLOID-BETA PEPTIDE (RESIDUES 10-35) | ||||||
Components | A-BETA AMYLOID | ||||||
Keywords | SUGAR BINDING PROTEIN / collapsed coil / hydrophobic cluster / hydrophobic patch | ||||||
Function / homology | Function and homology information 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 / response to interleukin-1 / positive regulation of mitotic cell cycle / extracellular matrix organization / adult locomotory behavior / 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 / microglial cell activation / synapse organization / regulation of long-term neuronal synaptic plasticity / 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 / neuron projection development / positive regulation of tumor necrosis factor production / cell-cell junction / synaptic vesicle Similarity search - Function | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing, and restrained molecular dynamics | ||||||
Authors | Zhang, S. / Iwata, K. / Lachenmann, M.J. / Peng, J.W. / Li, S. / Stimson, E.R. / Lu, Y. / Felix, A.M. / Maggio, J.E. / Lee, J.P. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2000 Title: The Alzheimer's peptide a beta adopts a collapsed coil structure in water. Authors: Zhang, S. / Iwata, K. / Lachenmann, M.J. / Peng, J.W. / Li, S. / Stimson, E.R. / Lu, Y. / Felix, A.M. / Maggio, J.E. / Lee, J.P. #1: Journal: Biochemistry / Year: 1995 Title: 1H NMR of A-Beta Amyloid Peptide Congeners in Water Solution. Conformational Changes Correlate with Plaque Competence. Authors: Lee, J.P. / Stimson, E.R. / Ghilardi, J.R. / Mantyh, P.W. / Lu, Y.A. / Felix, A.M. / Llanos, W. / Behbin, A. / Cummings, M. / Van Criekinge, M. / Timms, W. / Maggio, J.E. #2: Journal: Biophys.J. / Year: 2001 Title: Simulation Study of the Structure and Dynamics of the Alzheimer's Amyloid Peptide Congener in Solution. Authors: Massi, F. / Peng, J.W. / Lee, J.P. / Straub, J.E. #3: Journal: Proteins / Year: 2001 Title: Energy Landscape Theory for Alzheimer's Amyloid Beta-Peptide Fibril Elongation Authors: Massi, F. / Straub, J.E. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE The peptide residues are numbered 1-26 as they were designated in the distance-geometry ...SEQUENCE The peptide residues are numbered 1-26 as they were designated in the distance-geometry calculation. This corresponds to residues 10-35 of the "Human amyloid peptide Abeta." Abeta is a 40-43 residue peptide derived from the Human amyloid precursor protein (APP) (accession QRHUA4). Residue #10 in Abeta corresponds to residue #681 in APP, and residue #35 in Abeta corresponds to residue #706 in APP. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1hz3.cif.gz | 127.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1hz3.ent.gz | 103.6 KB | Display | PDB format |
PDBx/mmJSON format | 1hz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hz3_validation.pdf.gz | 354.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1hz3_full_validation.pdf.gz | 442.6 KB | Display | |
Data in XML | 1hz3_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 1hz3_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/1hz3 ftp://data.pdbj.org/pub/pdb/validation_reports/hz/1hz3 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein/peptide | Mass: 2907.345 Da / Num. of mol.: 1 / Fragment: RESIDUES 10-35 / Source method: obtained synthetically Details: This sequence is taken from the A-Beta peptide, which occurs naturally in Homo sapiens (human). The peptide was synthesized by Merrifield solid-phase methodology. References: UniProt: P05067 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||||||||||
NMR details | Text: Many observed intra-residue NOE-based distance constraints were not included in the structure calculations. |
-Sample preparation
Details |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample conditions | Ionic strength: <1mM / pH: 5.6 / Pressure: ambient / Temperature: 283 K | |||||||||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: distance geometry, simulated annealing, and restrained molecular dynamics Software ordinal: 1 Details: The structures are based on a total of 84 sequential, 66 medium- (i to i+2 or i+3) and 32 long-range NOE-derived distance constraints. | ||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 40 / Conformers submitted total number: 15 |