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Yorodumi- PDB-5boq: Human insulin with intra-chain chemical crosslink between modifie... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5boq | |||||||||
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Title | Human insulin with intra-chain chemical crosslink between modified B24 and B29 | |||||||||
Components | (Insulin) x 2 | |||||||||
Keywords | HORMONE / Chemical crosslink / B24-B29 / specificity | |||||||||
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 / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Brzozowski, A.M. / Turkenburg, J.P. / Jiracek, J. / Zakova, L. | |||||||||
Funding support | United Kingdom, Czech Republic, 2items
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Citation | Journal: Sci Rep / Year: 2016 Title: Rational steering of insulin binding specificity by intra-chain chemical crosslinking. Authors: Vikova, J. / Collinsova, M. / Kletvikova, E. / Budesinsky, M. / Kaplan, V. / Zakova, L. / Veverka, V. / Hexnerova, R. / Avino, R.J. / Strakova, J. / Selicharova, I. / Vanek, V. / Wright, D.W. ...Authors: Vikova, J. / Collinsova, M. / Kletvikova, E. / Budesinsky, M. / Kaplan, V. / Zakova, L. / Veverka, V. / Hexnerova, R. / Avino, R.J. / Strakova, J. / Selicharova, I. / Vanek, V. / Wright, D.W. / Watson, C.J. / Turkenburg, J.P. / Brzozowski, A.M. / Jiracek, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5boq.cif.gz | 52.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5boq.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 5boq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/5boq ftp://data.pdbj.org/pub/pdb/validation_reports/bo/5boq | HTTPS FTP |
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-Related structure data
Related structure data | 2n2vC 2n2wC 2n2xC 5bpoC 5bqqC 1msoS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 4 / Fragment: UNP residues 90-110 / Source method: obtained synthetically / Details: Sequence occurs naturally / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308 #2: Protein/peptide | Mass: 3408.885 Da / Num. of mol.: 4 / Fragment: UNP residues 25-54 / Source method: obtained synthetically / Details: covalent cross-link between modified B24 and B29 / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308 #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3 / Details: 0.1 M (NH4)2SO4, 1% (v/v) dioxane |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→41.28 Å / Num. all: 19860 / Num. obs: 19860 / % possible obs: 92.6 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.3 / % possible all: 60.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1mso Resolution: 1.7→60.01 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.338 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.12 / 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: 19.567 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→60.01 Å
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