+Open data
-Basic information
Entry | Database: PDB / ID: 1m5a | ||||||
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Title | Crystal Structure of 2-Co(2+)-Insulin at 1.2A Resolution | ||||||
Components |
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Keywords | HORMONE/GROWTH FACTOR / alpha helices / beta sheets / 3(10) helices / disulphide bridges / HORMONE-GROWTH FACTOR COMPLEX | ||||||
Function / homology | Function and homology information Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine ...Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine / positive regulation of lipoprotein lipase activity / lactate biosynthetic process / lipoprotein biosynthetic process / positive regulation of fatty acid biosynthetic process / positive regulation of glucose metabolic process / COPI-mediated anterograde transport / lipid biosynthetic process / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / 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 / positive regulation of glycogen biosynthetic process / positive regulation of DNA replication / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / negative regulation of lipid catabolic process / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of proteolysis / wound healing / insulin receptor binding / negative regulation of protein catabolic process / hormone activity / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / glucose homeostasis / insulin receptor signaling pathway / 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 / negative regulation of gene expression / positive regulation of cell population proliferation / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Nicholson, J.M. / Perkins, L.C. / Korber, F.C. | ||||||
Citation | Journal: Recent Research Developments in Molecular Biology / Year: 2006 Title: The high-resolution structure of hexameric T6 cobalt insulin: A possible pathway for the T to R transition. Authors: Nicholson, J.M. / Perkins, L.C. / Korber, F.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m5a.cif.gz | 36.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m5a.ent.gz | 27.8 KB | Display | PDB format |
PDBx/mmJSON format | 1m5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/1m5a ftp://data.pdbj.org/pub/pdb/validation_reports/m5/1m5a | HTTPS FTP |
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-Related structure data
Related structure data | 4insS 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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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations: z, x, y and y, z, x. |
-Components
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P01315 #2: Protein/peptide | Mass: 3403.927 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P01315 #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.51 % |
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Crystal grow | Temperature: 300 K / Method: slow cooling / pH: 6.3 Details: cobalt acetate, trisodium citrate, acetone, hydrochloric acid, pH 6.3, SLOW COOLING, temperature 300K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.2→20 Å / Num. all: 25860 / Num. obs: 25345 / % possible obs: 99.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.86 % / Rmerge(I) obs: 0.075 | ||||||||||||||||||
Reflection shell | Resolution: 1.2→1.28 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.354 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4INS Resolution: 1.2→20 Å / Isotropic thermal model: isotropic / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.029 Å / Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.23 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→20 Å
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Refine LS restraints |
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