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Yorodumi- PDB-2omq: VEALYL peptide derived from human insulin chain B, residues 12-17 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2omq | ||||||
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Title | VEALYL peptide derived from human insulin chain B, residues 12-17 | ||||||
Components | VEALYL peptide derived from human insulin chain B, residues 12-17 | ||||||
Keywords | PROTEIN FIBRIL / steric zipper / anti-parallel beta-sheet | ||||||
Function / homology | Function and homology information negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / insulin receptor binding / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / cognition / Golgi lumen / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / regulation of protein localization / glucose homeostasis / cell-cell signaling / insulin receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ivanova, M. / Sawaya, M.R. / Eisenberg, D. | ||||||
Citation | Journal: Nature / Year: 2007 Title: Atomic structures of amyloid cross-beta spines reveal varied steric zippers. Authors: Sawaya, M.R. / Sambashivan, S. / Nelson, R. / Ivanova, M.I. / Sievers, S.A. / Apostol, M.I. / Thompson, M.J. / Balbirnie, M. / Wiltzius, J.J. / McFarlane, H.T. / Madsen, A. / Riekel, C. / Eisenberg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2omq.cif.gz | 12.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2omq.ent.gz | 8.3 KB | Display | PDB format |
PDBx/mmJSON format | 2omq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/2omq ftp://data.pdbj.org/pub/pdb/validation_reports/om/2omq | HTTPS FTP |
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-Related structure data
Related structure data | 2okzC 2ol9C 2olxC 2ommC 2ompC 2on9C 2onaC 2onvC 2onwC 2onxC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | A steric zipper can be generated by repeated unit cell translations of the asymmetric unit along the b axis. |
-Components
#1: Protein/peptide | Mass: 706.827 Da / Num. of mol.: 4 / Fragment: residues 12-17 / Source method: obtained synthetically / References: UniProt: P01308*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 2.5 Details: 2mM peptide in 100 mM NaCl and 50 mM phosphate. Crystals can be more easily reproduced by dissolving peptide to 2 mM in water at room temperature, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9466 | ||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 16, 2005 | ||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9466 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→90 Å / Num. obs: 820 / % possible obs: 93 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.172 / Χ2: 1.065 / Net I/σ(I): 3.9 | ||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: polyalanine beta strands with ideal geometry Resolution: 2→21.84 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.375 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.293 / 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: 18.338 Å2
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Refinement step | Cycle: LAST / Resolution: 2→21.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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