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Yorodumi- PDB-5e7w: X-ray Structure of Human Recombinant 2Zn insulin at 0.92 Angstrom -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e7w | ||||||
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Title | X-ray Structure of Human Recombinant 2Zn insulin at 0.92 Angstrom | ||||||
Components | (Insulin) x 2 | ||||||
Keywords | IMMUNE SYSTEM / Insulin / human / recombinant / high-resolution | ||||||
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: 0.9519 Å | ||||||
Authors | Lisgarten, D.R. / Naylor, C.E. / Palmer, R.A. / Lobley, C.M.C. | ||||||
Citation | Journal: Chem Cent J / Year: 2017 Title: Ultra-high resolution X-ray structures of two forms of human recombinant insulin at 100 K. Authors: Lisgarten, D.R. / Palmer, R.A. / Lobley, C.M.C. / Naylor, C.E. / Chowdhry, B.Z. / Al-Kurdi, Z.I. / Badwan, A.A. / Howlin, B.J. / Gibbons, N.C.J. / Saldanha, J.W. / Lisgarten, J.N. / Basak, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e7w.cif.gz | 87.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e7w.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 5e7w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/5e7w ftp://data.pdbj.org/pub/pdb/validation_reports/e7/5e7w | HTTPS FTP |
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-Related structure data
Related structure data | 3w7yS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein/peptide , 2 types, 4 molecules ACBD
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Human Insulin A and C Chain Insulin was purchased from Insugen Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Komagataella pastoris (fungus) / References: UniProt: P01308 #2: Protein/peptide | Mass: 3433.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Human Insulin B and D chain Insulin was purchased from Insugen Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Komagataella pastoris (fungus) / References: UniProt: P01308 |
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-Non-polymers , 4 types, 224 molecules
#3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-POL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35 % / Description: needle |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 6.3 Details: The crystals were prepared by a batch method similar to that of Baker et al, 1988 [1], modified as follows: 0.01g of insulin as a fine powder was placed in a clean test tube; 0.02M HCl was ...Details: The crystals were prepared by a batch method similar to that of Baker et al, 1988 [1], modified as follows: 0.01g of insulin as a fine powder was placed in a clean test tube; 0.02M HCl was added to dissolve the protein; on addition of 0.15 mL of 0.15 M zinc acetate the solution became cloudy due to precipitation of the protein; 0.3 mL of acetone and then 0.5 mL of trisodium citrate together with 0.8 mL of water were added and the solution went clear; the pH was checked and increased with NaOH to a pH between 8 and 9 for different batches, thus ensuring complete dissolution. It was then adjusted to the required value of pH 6.3. If any slight turbidity occurred, it was removed by warming the solution. The solution was then filtered using a Millipore membrane/acetate cellulose acetate filter. This removes any nuclei which will encourage precipitation or formation of masses of small crystals. The solution was then warmed to 50 deg C by surrounding the test tube with preheated water in a Dewar. This allowed the solution to cool slowly to room temperature. The test tube was lightly sealed with cling film; crystals formed within a few days and were of suitable size for X-ray diffraction within two weeks; the test tube containing crystals was kept at 4 degC prior to data collection. The crystal used for data collection was about 0.2 mm3. PH range: 6.2 - 6.4 / Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.77 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2012 Details: Data were collected at 16000keV (0.77 Angstrom) and 100 deg K with the Pilatus 6M detector as close to the sample as possible (179.5mm). The EDNA strategy was used to obtain a start angle ...Details: Data were collected at 16000keV (0.77 Angstrom) and 100 deg K with the Pilatus 6M detector as close to the sample as possible (179.5mm). The EDNA strategy was used to obtain a start angle and 180 deg of data were collected with 0.1 deg oscillation and 0.1s exposure. The resolution of useful diffraction data achieved and used for structure analysis was 0.92 Angstrom. |
Radiation | Monochromator: Beamline fixed at 16000keV / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.77 Å / Relative weight: 1 |
Reflection | Resolution: 0.92→40.91 Å / Num. obs: 58647 / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 0.92→0.94 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.967 / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W7Y Resolution: 0.9519→10 Å / Cross valid method: FREE R-VALUE / σ(F): 0
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Displacement parameters | Biso mean: 18.45 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.9519→10 Å
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