+Open data
-Basic information
Entry | Database: PDB / ID: 1os4 | ||||||
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Title | Dehydrated T6 human insulin at 295 K | ||||||
Components | (Insulin) x 2 | ||||||
Keywords | HORMONE/GROWTH FACTOR / Air dried crystal / data measured at 298 K / HORMONE-GROWTH FACTOR COMPLEX | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Smith, G.D. / Blessing, R.H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Lessons from an aged, dried crystal of T(6) human insulin. Authors: Smith, G.D. / Blessing, R.H. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: The structure of T6 human insulin at 1.0 A resolution. Authors: Smith, G.D. / Pangborn, W.A. / Blessing, R.H. #2: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1988 Title: The structure of 2Zn pig insulin crystals at 1.5 A resoltuion. Authors: Baker, E.N. / Blundel, T.L. / Cutfield, J.F. / Cutfield, S.M. / Dodson, E.J. / Dodson, G.G. / Hodgkin, D.M.C. / Hubbard, R.E. / Isaacs, N.W. / Reynolds, C.D. #3: Journal: Acta Crystallogr.,Sect.B / Year: 1989 Title: Structure of insulin: Results of joint neutron and X-ray refinement. Authors: Wlodawer, A. / Savage, H. / Dodson, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1os4.cif.gz | 67.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1os4.ent.gz | 51.3 KB | Display | PDB format |
PDBx/mmJSON format | 1os4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1os4_validation.pdf.gz | 514.9 KB | Display | wwPDB validaton report |
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Full document | 1os4_full_validation.pdf.gz | 522.5 KB | Display | |
Data in XML | 1os4_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 1os4_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/1os4 ftp://data.pdbj.org/pub/pdb/validation_reports/os/1os4 | HTTPS FTP |
-Related structure data
Related structure data | 1os3C 4insS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a hexamer which is contained in the asymmetric unit. |
-Components
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 6 / Fragment: A-chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01308 #2: Protein/peptide | Mass: 3433.953 Da / Num. of mol.: 6 / Fragment: B-chain / Source method: isolated from a natural source / Source: (natural) 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: 2.12 Å3/Da / Density % sol: 41.43 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: slow cooling / pH: 6.3 Details: hydrochloric acid, zinc acetate, sodium citrate, acetone, pH 6.3, SLOW COOLING, temperature 295.K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 24, 2002 / Details: mirrors |
Radiation | Monochromator: Osmic confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→41.64 Å / Num. all: 15512 / Num. obs: 10252 / % possible obs: 82.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Biso Wilson estimate: 42.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.25→2.33 Å / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 1.6 / % possible all: 85.9 |
Reflection | *PLUS % possible obs: 82.7 % / Num. measured all: 15512 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 85.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 4INS Resolution: 2.25→41.64 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: Flat Model / Bsol: 65.3 Å2 / ksol: 0.41 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→41.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.029
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Refinement | *PLUS Lowest resolution: 41.7 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.31 |