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- PDB-3v19: Forestalling insulin fibrillation by insertion of a chiral clamp ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3v19 | ||||||
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Title | Forestalling insulin fibrillation by insertion of a chiral clamp mechanism-based application of protein engineering to global health | ||||||
![]() | (Insulin) x 2 | ||||||
![]() | HORMONE / zinc-binding site / long-acting insulin analog / receptor binding / protein engineering / insulin fibrillation | ||||||
Function / homology | ![]() 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 / 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 / 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 / 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 / endoplasmic reticulum lumen / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wan, Z.L. / Hua, Q.X. / Wickramasinghe, N.P. / Huang, K. / Petkova, A.T. / Hu, S.Q. / Phillips, N.B. / Yeh, I.J. / Whittake, J. / Ismail-Beigi, F. ...Wan, Z.L. / Hua, Q.X. / Wickramasinghe, N.P. / Huang, K. / Petkova, A.T. / Hu, S.Q. / Phillips, N.B. / Yeh, I.J. / Whittake, J. / Ismail-Beigi, F. / Katsoyyannis, P.G. / Tycko, R. / Weiss, M.A. | ||||||
![]() | ![]() Title: Forestalling insulin fibrillation by insertion of a chiral clamp mechanism-based application of protein engineering to global health Authors: Wan, Z.L. / Hua, Q.X. / Wickramasinghe, N.P. / Huang, K. / Petkova, A.T. / Hu, S.Q. / Phillips, N.B. / Yeh, I.J. / Whittake, J. / Ismail-Beigi, F. / Katsoyyannis, P.G. / Tycko, R. / Weiss, M.A. #1: ![]() Title: Diabetes-associated mutations in human insulin: crystal structure and photo-cross-linking studies of a-chain variant insulin Wakayama Authors: Wan, Z.L. / Huang, K. / Xu, B. / Hu, S.Q. / Wang, S. / Chu, Y.C. / Katsoyannis, P.G. / Weiss, M.A. #2: ![]() Title: Crystal structure of allo-Ile(A2)-insulin, an inactive chiral analogue: implications for the mechanism of receptor binding Authors: Wan, Z.L. / Xu, B. / Chu, Y.C. / Katsoyannis, P.G. / Weiss, M.A. #3: ![]() Title: Enhancing the activity of insulin at the receptor interface: crystal structure and photo-cross-linking of A8 analogues Authors: L Wan, Z. / Xu, B. / Chu, Y.C. / Li, B. / Nakagawa, S.H. / Qu, Y. / Hu, S.Q. / Katsoyannis, P.G. / Weiss, M.A. #4: ![]() 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. #5: ![]() Title: Structure of insulin in 4-zinc insulin Authors: Bentley, G. / Dodson, E. / Dodson, G. / Hodgkin, D. / Mercola, D. #6: ![]() Title: Phenol stabilizes more helix in a new symmetrical zinc insulin hexamer Authors: Derewenda, U. / Derewenda, Z. / Dodson, E. / Dodson, G. / Reynold, C. / Smith, G. / Sparks, C. / Swenson, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 35 KB | Display | ![]() |
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PDB format | ![]() | 24.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3v1gC ![]() 1rweS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 2434.768 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #2: Protein/peptide | Mass: 3433.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 4 types, 71 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/IPH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/IPH.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-IPH / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8 Details: 0.02 M Tris, 0.05 M sodium citrate, 5% acetone, 0.03% phenol, 0.01% zinc acetate, pH 8.0, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2007 / Details: Si 111 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9002 Å / Relative weight: 1 |
Reflection | Resolution: 2→16.69 Å / Num. all: 5596 / Num. obs: 5515 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 43.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 6.57 / Num. unique all: 798 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1RWE Resolution: 2→16.69 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: 42.7 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.18 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→16.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.034
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