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Yorodumi- PDB-4cy7: Crystal structure of human insulin analogue (NMe-AlaB8)-insulin c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cy7 | ||||||
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Title | Crystal structure of human insulin analogue (NMe-AlaB8)-insulin crystal form II | ||||||
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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 | 4cy7.cif.gz | 36.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cy7.ent.gz | 25.7 KB | Display | PDB format |
PDBx/mmJSON format | 4cy7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cy7_validation.pdf.gz | 467.3 KB | Display | wwPDB validaton report |
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Full document | 4cy7_full_validation.pdf.gz | 467.4 KB | Display | |
Data in XML | 4cy7_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 4cy7_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/4cy7 ftp://data.pdbj.org/pub/pdb/validation_reports/cy/4cy7 | HTTPS FTP |
-Related structure data
Related structure data | 2mpgC 4cxlC 4cxnC 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
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308 #2: Protein/peptide | Mass: 3462.006 Da / Num. of mol.: 2 / Mutation: YES / Source method: obtained synthetically Details: GLY8 IS SUBSTITUTED TO ALA AND N-PEPTIDE ATOM OF ALA8 IS METHYLATED Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308 #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-ACT / | #5: 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: 2.36 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | pH: 4 / Details: 0.0375 M NA2SO4, PH 4.0 |
-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: 1.4→32 Å / Num. obs: 21186 / % possible obs: 98.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.4 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 1.4→1.44 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.7 / % possible all: 98.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MSO Resolution: 1.4→31.97 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.063 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY RESIDUES B29-B30 ARE DISORDERED AND NOT MODELLED. THE TWO MOLECULES IN THE ASYMMETRIC UNIT DO NOT FORM ANY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY RESIDUES B29-B30 ARE DISORDERED AND NOT MODELLED. THE TWO MOLECULES IN THE ASYMMETRIC UNIT DO NOT FORM ANY PHYSIOLOGICAL DIMERS. THE PHYSIOLOGICAL DIMERS ARE FORMED BY CRYSTALLOGRAPHIC SYMMETRY. THE AB MOLECULE FORM DIMER WITH CRYSTALLOGRAPHIC SYMMETRY RELATED CD MOLECULE BY - XPLUSHALF,-Y,ZPLUSHALF THE CD MOLECULE FORM DIMER WITH CRYSTALLOGRAPHIC SYMMETRY RELATED AB MOLECULE BY THE SAME SYM OPERATOR
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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: 19.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→31.97 Å
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