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Yorodumi- PDB-4efx: Highly biologically active insulin with additional disulfide bond -
+Open data
-Basic information
Entry | Database: PDB / ID: 4efx | ||||||
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Title | Highly biologically active insulin with additional disulfide bond | ||||||
Components | (Insulin) x 2 | ||||||
Keywords | HORMONE | ||||||
Function / homology | Function and homology information negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic 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 peptide hormone secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic 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 peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / 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 / negative regulation of gluconeogenesis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / 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 / negative regulation of protein catabolic process / endosome lumen / positive regulation of glucose import / positive regulation of protein secretion / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / regulation of synaptic plasticity / vasodilation / hormone activity / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / glucose metabolic process / regulation of protein localization / glucose homeostasis / insulin receptor signaling pathway / cell-cell signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of NF-kappaB transcription factor activity / positive regulation of cell growth / protease binding / secretory granule lumen / 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 / Golgi membrane / endoplasmic reticulum lumen / 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 / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Norrman, M. / Vinther, T.N. | ||||||
Citation | Journal: Protein Sci. / Year: 2013 Title: Insulin analog with additional disulfide bond has increased stability and preserved activity. Authors: Vinther, T.N. / Norrman, M. / Ribel, U. / Huus, K. / Schlein, M. / Steensgaard, D.B. / Pedersen, T.A. / Pettersson, I. / Ludvigsen, S. / Kjeldsen, T. / Jensen, K.J. / Hubalek, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4efx.cif.gz | 31.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4efx.ent.gz | 21.8 KB | Display | PDB format |
PDBx/mmJSON format | 4efx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4efx_validation.pdf.gz | 451.3 KB | Display | wwPDB validaton report |
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Full document | 4efx_full_validation.pdf.gz | 454.7 KB | Display | |
Data in XML | 4efx_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 4efx_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/4efx ftp://data.pdbj.org/pub/pdb/validation_reports/ef/4efx | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 2373.683 Da / Num. of mol.: 2 / Mutation: A10C, B4C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308 #2: Protein/peptide | Mass: 3178.683 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308 #3: Chemical | #4: 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: 1.87 Å3/Da / Density % sol: 34.16 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.15M DL-Malic Acid, 20% w/v PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 12, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→50 Å / Num. all: 5517 / Num. obs: 5517 / % possible obs: 97 % / Redundancy: 5.3 % / Rsym value: 0.049 / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 1.98→2.01 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 205 / Rsym value: 0.202 / % possible all: 57.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: in house monomer model Resolution: 1.98→39.69 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.871 / SU B: 9.035 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.86 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→39.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.978→2.03 Å / Total num. of bins used: 20
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