+Open data
-Basic information
Entry | Database: PDB / ID: 5mam | ||||||
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Title | Human insulin in complex with serotonin | ||||||
Components |
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Keywords | HORMONE / serotonin / complex / specificity | ||||||
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 / Insulin processing / negative regulation of fatty acid metabolic process / 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 / Insulin processing / negative regulation of fatty acid metabolic process / 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 / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / negative regulation of protein secretion / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / fatty acid homeostasis / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic 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 long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / positive regulation of nitric-oxide synthase activity / 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 / hormone activity / negative regulation of protein catabolic process / cognition / positive regulation of neuron projection development / Golgi lumen / positive regulation of protein localization to nucleus / vasodilation / 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: 2.2 Å | ||||||
Authors | Brzozowski, A.M. / Turkenburg, J.P. / Jiracek, J. / Zakova, L. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Computational and structural evidence for neurotransmitter-mediated modulation of the oligomeric states of human insulin in storage granules. Authors: Palivec, V. / Viola, C.M. / Kozak, M. / Ganderton, T.R. / Krizkova, K. / Turkenburg, J.P. / Haluskova, P. / Zakova, L. / Jiracek, J. / Jungwirth, P. / Brzozowski, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mam.cif.gz | 164.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mam.ent.gz | 138 KB | Display | PDB format |
PDBx/mmJSON format | 5mam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/5mam ftp://data.pdbj.org/pub/pdb/validation_reports/ma/5mam | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein/peptide , 2 types, 32 molecules ACEGIKMOQSUWY024BDFHJLNPRTVXZ135
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 16 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308 #2: Protein/peptide | Mass: 3433.953 Da / Num. of mol.: 16 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308 |
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-Non-polymers , 4 types, 288 molecules
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-SRO / #6: 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: 2.2 Å3/Da / Density % sol: 43.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Zn-free human insulin was dissolved in 20 mM HCl at 5 mg/mL. The well solution contained 5 mM ZnAcetate, 35 mM NaCitrate, 1.1 M NaCl, 0.3M Tris pH 7.5, 40 mM serotonin. Hanging drops were ...Details: Zn-free human insulin was dissolved in 20 mM HCl at 5 mg/mL. The well solution contained 5 mM ZnAcetate, 35 mM NaCitrate, 1.1 M NaCl, 0.3M Tris pH 7.5, 40 mM serotonin. Hanging drops were set up in 1:1 protein:well volume ratios. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97631 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97631 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→51.18 Å / Num. obs: 36018 / % possible obs: 98.4 % / Redundancy: 4.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.46 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→51.18 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.21 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.269 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.744 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→51.18 Å
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