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Yorodumi- PDB-1j73: Crystal structure of an unstable insulin analog with native activity. -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j73 | ||||||
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Title | Crystal structure of an unstable insulin analog with native activity. | ||||||
Components |
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Keywords | HORMONE/GROWTH FACTOR / A8-Diaminobutyric Acid human insulin / hormone-receptor interface / 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: 2 Å | ||||||
Authors | Wan, Z. / Zhao, M. / Nakagawa, S. / Jia, W. / Weiss, M.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Non-standard insulin design: structure-activity relationships at the periphery of the insulin receptor. Authors: Weiss, M.A. / Wan, Z. / Zhao, M. / Chu, Y.C. / Nakagawa, S.H. / Burke, G.T. / Jia, W. / Hellmich, R. / Katsoyannis, P.G. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Diabetes-associated mutations in a beta-cell transcription factor destabilize an antiparallel "mini-zipper" in a dimerization interface Authors: Hua, Q.X. / Zhao, M. / Narayana, N. / Nakagawa, S.H. / Jia, W.H. / Weiss, M.A. #2: Journal: J.Mol.Biol. / Year: 1998 Title: The Relationship Between Insulin Bioactivity and Structure in the NH2-terminal A-chain Helix Authors: Olsen, H.B. / Ludvigsen, S. / Kaarsholm, N.C. #3: Journal: J.Mol.Biol. / Year: 1996 Title: Mapping the Functional Surface of Insulin by Design: Structure and Function of a Novel A-chain Analogue Authors: Hua, Q.X. / Hu, S.Q. / Frank, B.H. / Jia, W.H. / Chu, Y.C. / Wang, S.H. / Burke, G.T. / Kaysoyannis, P.G. / Weiss, M.A. #4: Journal: Biophys.Chem. / Year: 1994 Title: A Proposed Interaction Model of the Insulin Molecule with its Receptor Authors: Liang, D.C. / Chang, W.R. / Wan, Z.L. / Vijayan, N.M. | ||||||
History |
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Remark 400 | COMPOUND THE CONFORMATIONS OF TWO MONOMERS ARE DIFFERENT AS THE RESULT OF A CHANGE IN CONFORMATION ...COMPOUND THE CONFORMATIONS OF TWO MONOMERS ARE DIFFERENT AS THE RESULT OF A CHANGE IN CONFORMATION OF THE FIRST EIGHT RESIDUES OF THE B-CHAINS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j73.cif.gz | 30.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j73.ent.gz | 24 KB | Display | PDB format |
PDBx/mmJSON format | 1j73.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/1j73 ftp://data.pdbj.org/pub/pdb/validation_reports/j7/1j73 | 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
#1: Protein/peptide | Mass: 2382.713 Da / Num. of mol.: 2 / Mutation: T8(DAB) / Source method: obtained synthetically Details: The protein was chemically synthesized. The sequence is naturally found in Homo sapiens(human). References: UniProt: P01308 #2: Protein/peptide | Mass: 3433.953 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The protein was chemically synthesized. The sequence is naturally found in Homo sapiens(human). References: UniProt: P01308 #3: Chemical | #4: 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: 1.91 Å3/Da / Density % sol: 35.75 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: Tris, phonel, acetone, sodium citrate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 26, 1998 / Details: mirrors |
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→10 Å / Num. all: 5681 / Num. obs: 5448 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.05 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 611 % / Rmerge(I) obs: 0.097 / % possible all: 100 |
Reflection | *PLUS % possible obs: 93 % / Rmerge(I) obs: 0.056 |
-Processing
Software |
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Refinement | Resolution: 2→10 Å / σ(F): 2 / σ(I): 1
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 9.2 % / Rfactor obs: 0.205 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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