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Yorodumi- PDB-3fq9: Design of an insulin analog with enhanced receptor-binding select... -
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-Basic information
Entry | Database: PDB / ID: 3fq9 | ||||||
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Title | Design of an insulin analog with enhanced receptor-binding selectivity. Rationale, structure, and therapeutic implications | ||||||
Components | (Insulin) x 2 | ||||||
Keywords | HORMONE / receptor-binding / insulin design / rational / therapeutic implication / Carbohydrate metabolism / Cleavage on pair of basic residues / Diabetes mellitus / Disease mutation / Glucose metabolism / Pharmaceutical / Secreted | ||||||
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 / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Zhao, M. / Wan, Z.L. / Whittaker, L. / Xu, B. / Phillips, N. / Katsoyannis, P. / Whittaker, J. / Weiss, M.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Design of an insulin analog with enhanced receptor binding selectivity: rationale, structure, and therapeutic implications. Authors: Zhao, M. / Wan, Z.L. / Whittaker, L. / Xu, B. / Phillips, N.B. / Katsoyannis, P.G. / Ismail-Beigi, F. / Whittaker, J. / Weiss, M.A. #1: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1988 Title: The structure of 2zn pig insulin crystal 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. / Isaacs, N.W. / Reynolds, C.D. #2: Journal: Nature / Year: 1976 Title: Structure of insulin 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, G. / Reynold, C. / Smith, G. / Sparks, C. / Swenson, D. #4: Journal: J.Biol.Chem. / Year: 2006 Title: tpward the active conformation of insulin: stereospecific modelation of a structural swith in the B chain Authors: Hua, Q. / Nakagawa, S. / Hu, S.Q. / Jia, W. / Wang, S. / Weiss, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fq9.cif.gz | 52.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fq9.ent.gz | 38.2 KB | Display | PDB format |
PDBx/mmJSON format | 3fq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/3fq9 ftp://data.pdbj.org/pub/pdb/validation_reports/fq/3fq9 | HTTPS FTP |
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-Related structure data
Related structure data | 4insS 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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4 |
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5 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 2396.739 Da / Num. of mol.: 2 / Mutation: A1 is DAL, A8 is DAB / Source method: obtained synthetically Details: biosynthetic sequence based on Human Insulin A chain References: UniProt: P01308 #2: Protein/peptide | Mass: 3433.953 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: biosynthetic sequence based on Human Insulin B chain 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: 1.85 Å3/Da / Density % sol: 33.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.8 Details: 0.02M Tris, o.o5M soduim citrate, 5%acetone,0.03% phenol,0.01% zinc acetone, pH 7.8, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.948 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 26, 2001 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.948 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→40.92 Å / Num. all: 18393 / Num. obs: 18052 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.35→1.43 Å / Redundancy: 2.88 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 9.9 / Num. unique all: 2571 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4INS Resolution: 1.35→40.92 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 18 Å2
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Refine analyze | Luzzati coordinate error obs: 0.16 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.1 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→40.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.43 Å / Rfactor Rfree error: 0.015
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