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- PDB-7ac4: Structure of insulin collected by rotation serial crystallography... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ac4 | ||||||
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Title | Structure of insulin collected by rotation serial crystallography on a COC membrane at a synchrotron source | ||||||
![]() | (Insulin) x 2 | ||||||
![]() | HORMONE | ||||||
Function / homology | ![]() 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 / positive regulation of fatty acid biosynthetic process / positive regulation of glucose metabolic process / lipoprotein biosynthetic process / COPI-mediated anterograde transport / lipid biosynthetic process / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of protein autophosphorylation / positive regulation of DNA replication / positive regulation of protein secretion / insulin-like growth factor receptor binding / insulin receptor binding / hormone activity / glucose metabolic process / insulin receptor signaling pathway / glucose homeostasis / positive regulation of cell migration / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Martiel, I. / Padeste, C. / Karpik, A. / Huang, C.Y. / Vera, L. / Wang, M. / Marsh, M. | ||||||
![]() | ![]() Title: Versatile microporous polymer-based supports for serial macromolecular crystallography. Authors: Martiel, I. / Beale, J.H. / Karpik, A. / Huang, C.Y. / Vera, L. / Olieric, N. / Wranik, M. / Tsai, C.J. / Muhle, J. / Aurelius, O. / John, J. / Hogbom, M. / Wang, M. / Marsh, M. / Padeste, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46.6 KB | Display | ![]() |
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PDB format | ![]() | 33.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 249.7 KB | Display | ![]() |
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Full document | ![]() | 249.8 KB | Display | |
Data in XML | ![]() | 2.4 KB | Display | |
Data in CIF | ![]() | 3.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ac2C ![]() 7ac3C ![]() 7ac5C ![]() 7ac6C ![]() 7ai8C ![]() 7ai9C ![]() 5d53S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 3403.927 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-PGR / |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 50mM Na2HPO4, 10mM EDTA pH 10.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→38.98 Å / Num. obs: 13869 / % possible obs: 99.9 % / Redundancy: 7.16 % / CC1/2: 0.997 / Net I/σ(I): 8.26 |
Reflection shell | Resolution: 1.46→1.5 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1379 / CC1/2: 0.188 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5D53 Resolution: 1.46→38.98 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.49 / Stereochemistry target values: ML
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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 max: 145.7 Å2 / Biso mean: 32.0864 Å2 / Biso min: 12.69 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.46→38.98 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: -10.0079 Å / Origin y: -18.3949 Å / Origin z: -0.1924 Å
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Refinement TLS group |
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