+Open data
-Basic information
Entry | Database: PDB / ID: 4une | ||||||
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Title | Human insulin B26Phe mutant crystal structure | ||||||
Components |
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Keywords | HORMONE / B26 SITE | ||||||
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: 1.59 Å | ||||||
Authors | Zakova, L. / Klevtikova, E. / Lepsik, M. / Collinsova, M. / Watson, C.J. / Turkenburg, J.P. / Jiracek, J. / Brzozowski, A.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Human Insulin Analogues Modified at the B26 Site Reveal a Hormone Conformation that is Undetected in the Receptor Complex Authors: Zakova, L. / Klevtikova, E. / Lepsik, M. / Collinsova, M. / Watson, C.J. / Turkenburg, J.P. / Jiracek, J. / 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 | 4une.cif.gz | 35.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4une.ent.gz | 25 KB | Display | PDB format |
PDBx/mmJSON format | 4une.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4une_validation.pdf.gz | 450.3 KB | Display | wwPDB validaton report |
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Full document | 4une_full_validation.pdf.gz | 450.3 KB | Display | |
Data in XML | 4une_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 4une_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/4une ftp://data.pdbj.org/pub/pdb/validation_reports/un/4une | HTTPS FTP |
-Related structure data
Related structure data | 4ungC 4unhC 1msoS 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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3 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SEMISYNTHESISED, NOT RECOMBINANT / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308 #2: Protein/peptide | Mass: 3417.953 Da / Num. of mol.: 2 / Mutation: YES / Source method: obtained synthetically / Details: SEMISYNTHESISED, NOT RECOMBINANT / Source: (synth.) HOMO SAPIENS (human) / 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: 2.53 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | pH: 4 / Details: 0.15 M NA2SO4, PH 4.0, CP 5 MG/ML |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23 / Wavelength: 0.8726 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 11, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→50 Å / Num. obs: 13606 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.59→1.62 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 5.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MSO Resolution: 1.59→34.15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.305 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY THE TWO MOLECULES THAT ARE IN THE AU DO NOT FORM A PHYSIOLOGICAL DIMER. THE PHYSIOLOGICAL DIMERS FOR MOLECULE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY THE TWO MOLECULES THAT ARE IN THE AU DO NOT FORM A PHYSIOLOGICAL DIMER. THE PHYSIOLOGICAL DIMERS FOR MOLECULE AB (AND CD) IS (ARE) FORMED BY CRYSTALLOGRAPHIC SYMMETRY - X AND HALF,-Y,Z AND HALF
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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: 12.919 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→34.15 Å
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