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Yorodumi- PDB-7s4y: Serial Macromolecular Crystallography at ALBA Synchrotron Light S... -
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-Basic information
Entry | Database: PDB / ID: 7s4y | |||||||||
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Title | Serial Macromolecular Crystallography at ALBA Synchrotron Light Source - Insulin | |||||||||
Components |
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Keywords | HORMONE / Serial Crystallography | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | |||||||||
Authors | Martin-Garcia, J.M. / Botha, S. / Hu, H. / Jernigan, R. / Castellvi, A. / Lisova, S. / Gil, F. / Calisto, B. / Crespo, I. / Roy-Chowdbury, S. ...Martin-Garcia, J.M. / Botha, S. / Hu, H. / Jernigan, R. / Castellvi, A. / Lisova, S. / Gil, F. / Calisto, B. / Crespo, I. / Roy-Chowdbury, S. / Grieco, A. / Ketawala, G. / Weierstall, U. / Spence, J. / Fromme, P. / Zatsepin, N. / Boer, R. / Carpena, X. | |||||||||
Funding support | 2items
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Citation | Journal: J.Synchrotron Radiat. / Year: 2022 Title: Serial macromolecular crystallography at ALBA Synchrotron Light Source. Authors: Martin-Garcia, J.M. / Botha, S. / Hu, H. / Jernigan, R. / Castellvi, A. / Lisova, S. / Gil, F. / Calisto, B. / Crespo, I. / Roy-Chowdhury, S. / Grieco, A. / Ketawala, G. / Weierstall, U. / ...Authors: Martin-Garcia, J.M. / Botha, S. / Hu, H. / Jernigan, R. / Castellvi, A. / Lisova, S. / Gil, F. / Calisto, B. / Crespo, I. / Roy-Chowdhury, S. / Grieco, A. / Ketawala, G. / Weierstall, U. / Spence, J. / Fromme, P. / Zatsepin, N. / Boer, D.R. / Carpena, X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7s4y.cif.gz | 34.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s4y.ent.gz | 22.1 KB | Display | PDB format |
PDBx/mmJSON format | 7s4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7s4y_validation.pdf.gz | 442.7 KB | Display | wwPDB validaton report |
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Full document | 7s4y_full_validation.pdf.gz | 442.6 KB | Display | |
Data in XML | 7s4y_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 7s4y_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s4/7s4y ftp://data.pdbj.org/pub/pdb/validation_reports/s4/7s4y | HTTPS FTP |
-Related structure data
Related structure data | 7s4rC 7s4wC 7s4zC 7s50C 4ey9S C: citing same article (ref.) 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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2 |
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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.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Homo sapiens (human) / References: UniProt: P01308 #2: Protein/peptide | Mass: 3433.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Homo sapiens (human) / References: UniProt: P01308 #3: Chemical | #4: Chemical | ChemComp-CL / | #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: 1.85 Å3/Da / Density % sol: 33.52 % |
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Crystal grow | Temperature: 298 K / Method: batch mode Details: insulin was dissolved in 5 mM zinc chloride, 25 mM HCl at a concentration of 5-10 mg/ml. Cuboid-shaped microcrystals were obtained in 35.2 mM sodium citrate pH 7, and 5% (v/v) acetone as precipitant |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.27819 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.27819 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30.3 Å / Num. obs: 9140 / % possible obs: 100 % / Redundancy: 1292 % / Biso Wilson estimate: 29.1 Å2 / CC1/2: 0.9789 / CC star: 0.9947 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 881 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 928 / CC1/2: 0.36711 / CC star: 0.7328 / % possible all: 100 |
Serial crystallography sample delivery | Description: LCP Injector / Method: injection |
Serial crystallography sample delivery injection | Injector diameter: 5.0E-5 µm |
Serial crystallography data reduction | Frames total: 433986 / Lattices indexed: 51144 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EY9 Resolution: 1.71→24.35 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / SU B: 2.882 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.509 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→24.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.71→1.749 Å
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