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Yorodumi- PDB-8pi5: Crystal structure of human insulin desB30 precursor with an Alani... -
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-Basic information
Entry | Database: PDB / ID: 8pi5 | ||||||
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Title | Crystal structure of human insulin desB30 precursor with an Alanine-Methionine-Lysine C-peptide in hexamer (T3R3) conformation | ||||||
Components | Insulin B chain,Insulin A chain | ||||||
Keywords | HORMONE / insulin / precursor / dimer | ||||||
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 / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / 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 / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of respiratory burst / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / alpha-beta T cell activation / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / Signal attenuation / negative regulation of lipid catabolic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic 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 / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / positive regulation of glycolytic process / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / Regulation of insulin secretion / endosome lumen / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin-like growth factor receptor binding / wound healing / insulin receptor binding / regulation of synaptic plasticity / negative regulation of protein catabolic process / hormone activity / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / regulation of protein localization / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / 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 / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Johansson, E. / Schluckebier, G. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: Trends Biotechnol / Year: 2024 Title: Molecular engineering of insulin for recombinant expression in yeast. Authors: Kjeldsen, T. / Andersen, A.S. / Hubalek, F. / Johansson, E. / Kreiner, F.F. / Schluckebier, G. / Kurtzhals, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pi5.cif.gz | 81 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pi5.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 8pi5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pi5_validation.pdf.gz | 440.6 KB | Display | wwPDB validaton report |
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Full document | 8pi5_full_validation.pdf.gz | 441 KB | Display | |
Data in XML | 8pi5_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 8pi5_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/8pi5 ftp://data.pdbj.org/pub/pdb/validation_reports/pi/8pi5 | HTTPS FTP |
-Related structure data
Related structure data | 8pi4C 8pi6C 8pjcC 8pjhC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 6029.985 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-RCO / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.52 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 6 mg/ml protein, 20 mM resorcinol, 0.5 Zn2+ (from zinc acetate) per insuln monomer in water, pH 7.95 precipitant: 0.1 M Bicine, pH 9.0, 2 % (v/v) 1,4-dioxane, 10 % (w/v) PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→13.66 Å / Num. obs: 10563 / % possible obs: 97.17 % / Redundancy: 6.1 % / Biso Wilson estimate: 21.26 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.04731 / Rpim(I) all: 0.01975 / Rrim(I) all: 0.05135 / Net I/σ(I): 25.54 |
Reflection shell | Resolution: 1.66→1.72 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.3121 / Mean I/σ(I) obs: 3.58 / Num. unique obs: 829 / CC1/2: 0.847 / CC star: 0.958 / Rpim(I) all: 0.2031 / Rrim(I) all: 0.375 / % possible all: 76.19 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→13.66 Å / SU ML: 0.1539 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.8241 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.36 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→13.66 Å
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Refine LS restraints |
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LS refinement shell |
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