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Yorodumi- PDB-8pi6: Crystal structure of the monomeric zinc free human insulin A22K, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pi6 | ||||||
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Title | Crystal structure of the monomeric zinc free human insulin A22K, B3E, B26E, B29R, desB30 precursor with a Ser-Glu-Asp-Trp-Trp-Arg C-peptide and a Glu-Glu-Gly-Glu-Pro-Arg N-terminal extension | ||||||
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 / 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 peptide hormone secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic 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 peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / 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 / negative regulation of gluconeogenesis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / 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 / negative regulation of protein catabolic process / endosome lumen / positive regulation of glucose import / positive regulation of protein secretion / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / regulation of synaptic plasticity / vasodilation / hormone activity / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / glucose metabolic process / regulation of protein localization / glucose homeostasis / insulin receptor signaling pathway / cell-cell signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of NF-kappaB transcription factor activity / positive regulation of cell growth / protease binding / secretory granule lumen / 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 / Golgi membrane / endoplasmic reticulum lumen / 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 / SAD / Resolution: 2.14 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 | 8pi6.cif.gz | 149.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pi6.ent.gz | 100.3 KB | Display | PDB format |
PDBx/mmJSON format | 8pi6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pi6_validation.pdf.gz | 464.8 KB | Display | wwPDB validaton report |
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Full document | 8pi6_full_validation.pdf.gz | 468.6 KB | Display | |
Data in XML | 8pi6_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 8pi6_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/8pi6 ftp://data.pdbj.org/pub/pdb/validation_reports/pi/8pi6 | HTTPS FTP |
-Related structure data
Related structure data | 8pi4C 8pi5C 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
#1: Protein | Mass: 7396.271 Da / Num. of mol.: 5 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: 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 | Density Matthews: 1.95 Å3/Da / Density % sol: 37.06 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 8 mg/ml protein in water precipitant: 0.1 M sodium citrate, pH 5.6, 1.o M ammonium phosphate monobasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.075 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→45.88 Å / Num. obs: 14677 / % possible obs: 84.68 % / Redundancy: 109.8 % / Biso Wilson estimate: 41.94 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.01512 / Rrim(I) all: 0.1727 / Net I/σ(I): 33.01 |
Reflection shell | Resolution: 2.14→2.219 Å / Redundancy: 16.1 % / Rmerge(I) obs: 2.496 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 726 / CC1/2: 0.0712 / CC star: 0.365 / Rpim(I) all: 0.5138 / Rrim(I) all: 2.562 / % possible all: 44.84 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.14→45.88 Å / SU ML: 0.2676 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 34.4413 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: 62.09 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→45.88 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 60.4524471165 Å / Origin y: 65.770051835 Å / Origin z: 82.5634760152 Å
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Refinement TLS group | Selection details: all |