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Yorodumi- PDB-3zs2: TyrB25,NMePheB26,LysB28,ProB29-insulin analogue crystal structure -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zs2 | |||||||||
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Title | TyrB25,NMePheB26,LysB28,ProB29-insulin analogue crystal structure | |||||||||
Components |
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Keywords | HORMONE / CARBOHYDRATE METABOLISM / GLUCOSE METABOLISM / DIABETES MELLITUS | |||||||||
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: 1.97 Å | |||||||||
Authors | Antolikova, E. / Zakova, L. / Turkenburg, J.P. / Watson, C.J. / Hanclova, I. / Sanda, M. / Cooper, A. / Kraus, T. / Brzozowski, A.M. / Jiracek, J.A. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Non-Equivalent Role of Inter- and Intramolecular Hydrogen Bonds in the Insulin Dimer Interface. Authors: Antolikova, E. / Zakova, L. / Turkenburg, J.P. / Watson, C.J. / Hanclova, I. / Sanda, M. / Cooper, A. / Kraus, T. / Brzozowski, A.M. / Jiracek, J.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zs2.cif.gz | 110.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zs2.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zs2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zs2_validation.pdf.gz | 529.1 KB | Display | wwPDB validaton report |
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Full document | 3zs2_full_validation.pdf.gz | 891.1 KB | Display | |
Data in XML | 3zs2_validation.xml.gz | 64.4 KB | Display | |
Data in CIF | 3zs2_validation.cif.gz | 75.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/3zs2 ftp://data.pdbj.org/pub/pdb/validation_reports/zs/3zs2 | HTTPS FTP |
-Related structure data
Related structure data | 3zqrC 1ms0S 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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Unit cell |
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-Components
-Protein/peptide , 2 types, 12 molecules ACEGIKBDFHJL
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 6 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308 #2: Protein/peptide | Mass: 3447.980 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308 |
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-Non-polymers , 4 types, 160 molecules
#3: Chemical | ChemComp-IPH / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE N-PEPTIDE ATOM OF B26PHE IS METHYLATED |
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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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | pH: 8.2 Details: 0.1 M NACITRATE, 0.3 M TRIS PH 8.2, 0.6 MM ZN(AC)2, 0.06% PHENOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 1.0712 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 3, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0712 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. obs: 18615 / % possible obs: 90.2 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 8.5 / % possible all: 61.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MS0 Resolution: 1.97→53.68 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.412 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
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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: 40.213 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→53.68 Å
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