+Open data
-Basic information
Entry | Database: PDB / ID: 4cxl | ||||||
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Title | Human insulin analogue (D-ProB8)-insulin | ||||||
Components |
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Keywords | HORMONE / DIABETES | ||||||
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 / negative regulation of fatty acid metabolic process / Insulin processing / 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 / negative regulation of fatty acid metabolic process / Insulin processing / 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 / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic 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 nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / 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 / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / cognition / Golgi lumen / vasodilation / positive regulation of protein localization to nucleus / 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: 1.5 Å | ||||||
Authors | Kosinova, L. / Veverka, V. / Novotna, P. / Collinsova, M. / Urbanova, M. / Jiracek, J. / Moody, N.R. / Turkenburg, J.P. / Brzozowski, A.M. / Zakova, L. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: An Insight Into Structural and Biological Relevance of the T/R Transition of the B-Chain N-Terminus in Human Insulin. Authors: Kosinova, L. / Veverka, V. / Novotna, P. / Collinsova, M. / Urbanova, M. / Moody, N.R. / Turkenburg, J.P. / Jiracek, J. / Brzozowski, A.M. / Zakova, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cxl.cif.gz | 24.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cxl.ent.gz | 15.9 KB | Display | PDB format |
PDBx/mmJSON format | 4cxl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/4cxl ftp://data.pdbj.org/pub/pdb/validation_reports/cx/4cxl | HTTPS FTP |
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-Related structure data
Related structure data | 2mpgC 4cxnC 4cy7C 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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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: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308 |
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#2: Protein/peptide | Mass: 3474.016 Da / Num. of mol.: 1 / Mutation: YES / Source method: obtained synthetically Details: GLY OF B8 SITE IS REPLACED BY D-AMINO ACID D-PROLINE Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308 |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 67 % / Description: NONE |
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Crystal grow | pH: 8 Details: 0.1 M TRIS/HCL PH 8.0, 0.2 SODIUM CITRATE, 40% V/V MPD, PROTEIN CONCENTRATION 5MG/ML IN 20 MM HCL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 16, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→39.33 Å / Num. obs: 13097 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 20 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 31.8 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 20 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MSO Resolution: 1.5→39.33 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.132 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. B30 THR IS NOT VISIBLE AND NOT MODELLED
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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: 26.337 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→39.33 Å
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