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Yorodumi- PDB-1jca: Non-standard Design of Unstable Insulin Analogues with Enhanced A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jca | ||||||
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Title | Non-standard Design of Unstable Insulin Analogues with Enhanced Activity | ||||||
Components |
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Keywords | HORMONE/GROWTH FACTOR / A8-Lysine human insulin / insulin receptor / 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 / 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 ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic 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 respiratory burst / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / alpha-beta T cell activation / 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 / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic 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 / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / positive regulation of glycolytic process / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / Regulation of insulin secretion / acute-phase response / endosome lumen / positive regulation of protein secretion / positive regulation of glucose import / positive regulation of cell differentiation / negative regulation of proteolysis / regulation of transmembrane transporter activity / insulin-like growth factor receptor binding / wound healing / insulin receptor binding / regulation of synaptic plasticity / negative regulation of protein catabolic process / hormone activity / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / regulation of protein localization / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / 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 / FOURIER SYNTHESIS / Resolution: 2.5 Å | ||||||
Authors | Weiss, M.A. / Wan, Z. / Zhao, M. / Chu, Y.-C. / Nakagawa, S.H. / Burke, G.T. / Jia, W. / Hellmich, R. / Katsoyannis, P.G. | ||||||
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: BIOPHYS.CHEM. / Year: 1994 Title: A Proposed Interaction Model of Insulin Molecules with its Receptor Authors: Liang, D.C. / Chang, W.R. / Wan, Z.L. / Vijayan, N.M. #2: 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. / Weiss, M.A. #3: 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. #4: Journal: J.Mol.Biol. / Year: 1996 Title: Mapping the Functional Surface of Insulin by Design: Structure and Function of Novel A-chain Analogue Authors: Hua, Q.X. / Hu, S.Q. / Frank, B.H. / Jia, W. / Chu, Y.C. / Wang, S.H. / Burke, G.T. / Katsoyannis, P.G. / Weiss, M.A. | ||||||
History |
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Remark 400 | COMPOUND The crystallographic asymmetric unit of insulin consists of two insulin monomers each ...COMPOUND The crystallographic asymmetric unit of insulin consists of two insulin monomers each consisting of two heterochains. The entry presents coordinates for monomer 1 (chain indicators A and B) and monomer 2 (chain indicators C and D). There are two zinc ions per insulin hexamer located on the three-fold axis. The conformations of two monomers are different as the result of a change in conformation of the first eight residues of the B-chain. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jca.cif.gz | 33.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jca.ent.gz | 23.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jca_validation.pdf.gz | 369.6 KB | Display | wwPDB validaton report |
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Full document | 1jca_full_validation.pdf.gz | 369.6 KB | Display | |
Data in XML | 1jca_validation.xml.gz | 3.2 KB | Display | |
Data in CIF | 1jca_validation.cif.gz | 4.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/1jca ftp://data.pdbj.org/pub/pdb/validation_reports/jc/1jca | HTTPS FTP |
-Related structure data
Related structure data | 1j73C 1trzS 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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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations: -y, x-y, z and -x+y, -x, z. |
-Components
#1: Protein/peptide | Mass: 2411.774 Da / Num. of mol.: 2 / Mutation: T8K / Source method: obtained synthetically Details: This peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (humans). References: UniProt: P01308 #2: Protein/peptide | Mass: 3433.953 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: This peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (humans). 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: 2.03 Å3/Da / Density % sol: 39.43 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: Tris, sodium citrate, acetone, phenol, pH 7.0, VAPOR DIFFUSION, HANGING DROP Temp details: ambient | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 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: Jan 1, 2000 / Details: mirrors |
Radiation | Monochromator: MIRROR / 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→10 Å / Num. all: 3369 / Num. obs: 3169 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.071 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.16 / % possible all: 97.5 |
Reflection | *PLUS Rmerge(I) obs: 0.076 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1TRZ Resolution: 2.5→10 Å / σ(F): 2 / σ(I): 1
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.204 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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