[English] 日本語
Yorodumi- PDB-3jsd: Insulin's biosynthesis and activity have opposing structural requ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jsd | ||||||
---|---|---|---|---|---|---|---|
Title | Insulin's biosynthesis and activity have opposing structural requirements: a new factor in neonatal diabetes mellitus | ||||||
Components |
| ||||||
Keywords | HORMONE / diabetes mellitus / Insulin's biosynthesis / proinsulin / insulin hexamer / Carbohydrate metabolism / Cleavage on pair of basic residues / Disease mutation / Disulfide bond / Glucose metabolism / Secreted | ||||||
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 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Weiss, M.A. / Wan, Z.L. / Dodson, E.J. / Liu, M. / Xu, B. / Hua, Q.X. / Turkenburg, M. / Whittingham, J. / Nakagawa, S.H. / Huang, K. ...Weiss, M.A. / Wan, Z.L. / Dodson, E.J. / Liu, M. / Xu, B. / Hua, Q.X. / Turkenburg, M. / Whittingham, J. / Nakagawa, S.H. / Huang, K. / Hu, S.Q. / Jia, W.H. / Wang, S.H. / Brange, J. / Whittaker, J. / Arvan, P. / Katsoyannis, P.G. / Dodson, G.G. | ||||||
Citation | Journal: To be Published Title: Insulin's biosynthesis and activity have opposing structural requirements: a new factor in neonatal diabetes mellitus Authors: Weiss, M.A. / Wan, Z.L. / Dodson, E.J. / Liu, M. / Xu, B. / Hua, Q.X. / Turkenburg, M. / Whittingham, J. / Nakagawa, S.H. / Huang, K. / Hu, S.Q. / Jia, W.H. / Wang, S.H. / Brange, J. / ...Authors: Weiss, M.A. / Wan, Z.L. / Dodson, E.J. / Liu, M. / Xu, B. / Hua, Q.X. / Turkenburg, M. / Whittingham, J. / Nakagawa, S.H. / Huang, K. / Hu, S.Q. / Jia, W.H. / Wang, S.H. / Brange, J. / Whittaker, J. / Arvan, P. / Katsoyannis, P.G. / Dodson, G.G. #1: Journal: Philos.Trans.R.Soc.Lond.B Biol.Sci. / Year: 1988 Title: The structure of 2Zn pig insulin crystals at 1.5 A resolution. Authors: Baker, E.N. / Blundell, T.L. / Cutfield, J.F. / Cutfield, S.M. / Dodson, E.J. / Dodson, G.G. / Hodgkin, D.M. / Hubbard, R.E. / Isaacs, N.W. / Reynolds, C.D. #2: Journal: Nature / Year: 1976 Title: Structure of insulin in 4-zinc insulin. Authors: Bentley, G. / Dodson, E. / Dodson, G. / Hodgkin, D. / Mercola, D. #3: 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. #4: Journal: J.Biol.Chem. / Year: 2006 Title: Toward the active conformation of insulin: stereospecific modulation of a structural switch in the B chain. Authors: Hua, Q.X. / Nakagawa, S. / Hu, S.Q. / Jia, W. / Wang, S. / Weiss, M.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3jsd.cif.gz | 33.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3jsd.ent.gz | 23 KB | Display | PDB format |
PDBx/mmJSON format | 3jsd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jsd_validation.pdf.gz | 422.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3jsd_full_validation.pdf.gz | 424.1 KB | Display | |
Data in XML | 3jsd_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | 3jsd_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/3jsd ftp://data.pdbj.org/pub/pdb/validation_reports/js/3jsd | HTTPS FTP |
-Related structure data
Related structure data | 3rovC 1trzS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-Components
-Protein/peptide , 2 types, 4 molecules ACBD
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 2 / Fragment: UNP residues 90-110 / Source method: obtained synthetically / Details: biosynthetic sequence / References: UniProt: P01308 #2: Protein/peptide | Mass: 3447.979 Da / Num. of mol.: 2 / Fragment: UNP residues 25-54 / Source method: obtained synthetically / Details: biosynthetic sequence / References: UniProt: P01308 |
---|
-Non-polymers , 4 types, 23 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-IPH / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.27 % Description: The structure factor file contains Friedel pairs |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8 Details: 0.02M Tris-HCl, 0.05M Sodium citrate, 5% Acetone, 0.03% Phenol, 0.01% Zinc acetate, pH 8.0, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 25, 1998 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→17.37 Å / Num. all: 7390 / Num. obs: 3190 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.071 |
Reflection shell | Resolution: 2.5→2.66 Å / Rmerge(I) obs: 0.254 / Num. unique all: 455 / % possible all: 95.2 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1TRZ Resolution: 2.5→17.37 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.7 Å2
| |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.31 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→17.37 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2
|