+Open data
-Basic information
Entry | Database: PDB / ID: 3zi3 | ||||||
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Title | Crystal structure of the B24His-insulin - human analogue | ||||||
Components | (INSULIN) x 2 | ||||||
Keywords | HORMONE | ||||||
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 | Zakova, L. / Kletvikova, E. / Veverka, V. / Lepsik, M. / Watson, C.J. / Turkenburg, J.P. / Jiracek, J. / Brzozowski, A.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural Integrity of the B24 Site in Human Insulin is Important for Hormone Functionality Authors: Zakova, L. / Kletvikova, E. / Veverka, V. / Lepsik, M. / Watson, C.J. / Turkenburg, J.P. / Jiracek, J. / Brzozowski, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zi3.cif.gz | 20.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zi3.ent.gz | 12.8 KB | Display | PDB format |
PDBx/mmJSON format | 3zi3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/3zi3 ftp://data.pdbj.org/pub/pdb/validation_reports/zi/3zi3 | HTTPS FTP |
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-Related structure data
Related structure data | 2m2mC 2m2nC 2m2oC 2m2pC 1msoS S: Starting model for refinement 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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Components on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SEMISYNTHESIS / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308 |
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#2: Protein/peptide | Mass: 3424.926 Da / Num. of mol.: 1 / Mutation: YES / Source method: obtained synthetically / Details: SEMISYNTHESIS / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308 |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Sequence details | PHEB24 IN CHAIN B IS REPLACED IN THIS ANALOGUE BY HIS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 41 % / Description: NONE |
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Crystal grow | pH: 3 / Details: 0.075 M LI2SO4, PH 3.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→28 Å / Num. obs: 5435 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 12.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3.9 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MSO Resolution: 1.7→28.1 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.283 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY. RESIDUES B1 AND B21-B30 ARE DISORDERED RESIDUES B1 AND B21- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY. RESIDUES B1 AND B21-B30 ARE DISORDERED RESIDUES B1 AND B21-B30 ARE DISORDERED HENCE NOT INCLUDED IN THE MODEL. ONLY THE CALPHA AND CO ATOMS FOR GLUB21 HAVE BEEN MODELLED. TYRB16 IS VERY MOBILE WITH ONLY SOME TERMINAL DENSITY FOR ITS SIDE CHAIN MISSING. THERE IS A LONG TUBULAR ELECTRON DENSITY NEXT TO, FOR EXAMPLE, GLUA4 SIDE CHAIN. AS IT APPEARS ALONG THE 4-FOLD AXIS, DOES NOT REPRESENT ANY CRYSTALLISATION SOLVENT, AND IS NOT A PART OF THE PROTEIN IS HAS BEEN LEFT UNMODELLED.
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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: 35.757 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→28.1 Å
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