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Yorodumi- PDB-1ev3: Structure of the rhombohedral form of the M-cresol/insulin R6 hexamer -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ev3 | ||||||
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Title | Structure of the rhombohedral form of the M-cresol/insulin R6 hexamer | ||||||
Components | (INSULIN) x 2 | ||||||
Keywords | HORMONE/GROWTH FACTOR / R6 Hexamer / 18-A / HORMONE-GROWTH FACTOR COMPLEX | ||||||
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 / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / 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 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.78 Å | ||||||
Authors | Smith, G.D. / Ciszak, E. / Magrum, L.A. / Pangborn, W.A. / Blessing, R.H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: R6 hexameric insulin complexed with m-cresol or resorcinol. Authors: Smith, G.D. / Ciszak, E. / Magrum, L.A. / Pangborn, W.A. / Blessing, R.H. #1: Journal: Proteins / Year: 1992 Title: Structure of a Rhombohedral R6 Insulin/Phenol Complex Authors: Smith, G.D. / Dodson, G.G. #2: Journal: Nature / Year: 1989 Title: Phenol Stabilizes more Helix in a new Symmetrical Zinc Insulin Hexamer Authors: Derewenda, U. / Derewenda, Z. / Dodson, E.J. / Dodson, G.G. / Reynolds, C.D. / Smith, G.D. / Sparks, C. / Swenson, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ev3.cif.gz | 30.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ev3.ent.gz | 24.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ev3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/1ev3 ftp://data.pdbj.org/pub/pdb/validation_reports/ev/1ev3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein/peptide , 2 types, 4 molecules ACBD
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 2 / Fragment: RESIDUES 87-107 / Source method: obtained synthetically Details: This sequence occurs naturally in homo sapiens (human) References: UniProt: P01308 #2: Protein/peptide | Mass: 3433.953 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-54 / Source method: obtained synthetically Details: This sequence occurs naturally in homo sapiens (human) References: UniProt: P01308 |
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-Non-polymers , 4 types, 95 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.03 Å3/Da / Density % sol: 39.41 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: slow cooling / pH: 8.5 Details: 30 mg insulin, 3.0 ml of 0.02 M HCl, 0.3 ml of 0.15 M Zinc Acetate, 1.5 ml of 0.2 M Sodium Citrate, 1.2 ml of 2.5% m-cresol in acetone, 0.36 gm sodium chloride, pH 8.5, SLOW COOLING, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 13, 2000 / Details: OSMIC CONFOCAL MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19.72 Å / Num. all: 9334 / Num. obs: 9334 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 60.6 |
Reflection shell | Resolution: 1.78→1.83 Å / Redundancy: 3 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 10 / % possible all: 82.6 |
Reflection | *PLUS Num. measured all: 64359 |
Reflection shell | *PLUS % possible obs: 82.6 % |
-Processing
Software |
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Refinement | Resolution: 1.78→19.72 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.69 Å2 / ksol: 0.342 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.78→19.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.89 Å / Rfactor Rfree error: 0.32 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.3 % / Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 33.2 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.371 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.336 / Rfactor obs: 0.336 |