+Open data
-Basic information
Entry | Database: PDB / ID: 1zni | ||||||
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Title | INSULIN | ||||||
Components | (INSULIN) x 2 | ||||||
Keywords | HORMONE / GLUCOSE METABOLISM | ||||||
Function / homology | Function and homology information Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine ...Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine / positive regulation of lipoprotein lipase activity / lactate biosynthetic process / lipoprotein biosynthetic process / positive regulation of fatty acid biosynthetic process / positive regulation of glucose metabolic process / COPI-mediated anterograde transport / lipid biosynthetic process / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / 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 / positive regulation of glycogen biosynthetic process / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / negative regulation of lipid catabolic process / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / positive regulation of DNA replication / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of proteolysis / wound healing / insulin receptor binding / negative regulation of protein catabolic process / hormone activity / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / glucose homeostasis / insulin receptor signaling pathway / 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 / negative regulation of gene expression / positive regulation of cell population proliferation / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.498 Å | ||||||
Authors | Turkenburg, M.G.W. / Whittingham, J.L. / Dodson, G.G. / Dodson, E.J. / Xiao, B. / Bentley, G.A. | ||||||
Citation | Journal: Nature / Year: 1976 Title: Structure of insulin in 4-zinc insulin. Authors: Bentley, G. / Dodson, E. / Dodson, G. / Hodgkin, D. / Mercola, D. #1: Journal: Biopolymers / Year: 1992 Title: The Structure of a Rhombohedral R6 Insulin Hexamer that Binds Phenol Authors: Smith, G.D. / Dodson, G.G. #2: Journal: J.Mol.Biol. / Year: 1992 Title: Role of B13 Glu in Insulin Assembly. The Hexamer Structure of Recombinant Mutant (B13 Glu-->Gln) Insulin Authors: Bentley, G.A. / Brange, J. / Derewenda, Z. / Dodson, E.J. / Dodson, G.G. / Markussen, J. / Wilkinson, A.J. / Wollmer, A. / Xiao, B. #3: Journal: J.Mol.Biol. / Year: 1991 Title: X-Ray Analysis of the Single Chain B29-A1 Peptide-Linked Insulin Molecule. A Completely Inactive Analogue Authors: Derewenda, U. / Derewenda, Z. / Dodson, E.J. / Dodson, G.G. / Xiao, B. / Markussen, J. #4: Journal: Nature / Year: 1989 Title: Phenol Stabilizes More Helix in a New Symmetrical Zinc Insulin Hexamer Authors: Derewenda, U. / Derewenda, Z. / Dodson, E.J. / Dodson, G.G. / Reynolds, C.D. / Smith, G.D. / Sparks, C. / Swenson, D. #5: Journal: Biochemistry / Year: 1989 Title: Comparison of Solution Structural Flexibility and Zinc Binding Domains for Insulin, Proinsulin, and Miniproinsulin Authors: Kaarsholm, N.C. / Ko, H.C. / Dunn, M.F. #6: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1988 Title: The Structure of 2Zn Pig Insulin Crystals 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.M. / Hubbard, R.E. / Isaacs, N.W. / Reynolds, C.D. / Sakabe, K. / Sakabe, N. / Vijayan, N.M. #7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1984 Title: Structural Stability in the 4-Zinc Human Insulin Hexamer Authors: Smith, G.D. / Swenson, D.C. / Dodson, E.J. / Dodson, G.G. / Reynolds, C.D. #8: Journal: J.Mol.Biol. / Year: 1978 Title: Rhombohedral Insulin Crystal Transformation Authors: Bentley, G. / Dodson, G. / Lewitova, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zni.cif.gz | 33.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zni.ent.gz | 26.2 KB | Display | PDB format |
PDBx/mmJSON format | 1zni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/1zni ftp://data.pdbj.org/pub/pdb/validation_reports/zn/1zni | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.88898, -0.45231, -0.07163), Details | IN 2ZN INSULIN (ENTRY 4INS) THE FOLLOWING APPLIES: THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT OF INSULIN CONSISTS OF TWO INSULIN MOLECULES EACH CONSISTING OF TWO CHAINS. ENTRY 4INS PRESENTS COORDINATES FOR MOLECULES I (CHAIN IDENTIFIERS *A* AND *B*) AND II (CHAIN IDENTIFIERS *C* AND *D*). THE QUASI-TWO-FOLD AXIS THAT TRANSFORMS MOLECULE I INTO MOLECULE II IS GIVEN IN THE *MTRIX* RECORDS. APPLYING THE THREE-FOLD CRYSTALLOGRAPHIC AXIS YIELDS A HEXAMER AROUND THE AXIS. THERE ARE TWO ZINC IONS SITUATED ON THIS THREE-FOLD AXIS. COORDINATES FOR THE ZINC IONS AND SOME WATER MOLECULES ARE INCLUDED WITH A BLANK CHAIN IDENTIFIER. | |
-Components
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P01315 #2: Protein/peptide | Mass: 3403.927 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P01315 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | THE QUASI-TWO-FOLD SYMMETRY BREAKS DOWN MOST SERIOUSLY AT RESIDUES PHE B 1 TO CYS B 7 AND PHE D 1 ...THE QUASI-TWO-FOLD SYMMETRY BREAKS DOWN MOST SERIOUSLY AT RESIDUES PHE B 1 TO CYS B 7 AND PHE D 1 TO CYS D 7 PHE B 25 AND PHE D 25 | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.56 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5 / Method: batch method / Details: Harding, M.M., (1966) J. Mol. Biol., 16, 212. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Biso Wilson estimate: 21.1 Å2 |
-Processing
Software | Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.498→40 Å / σ(F): 0 Details: REFINEMENT TOOK PLACE OVER A PERIOD OF MORE THAN 20 YEARS. SOME RESIDUES ARE APPARENTLY DISORDERED AND CERTAINLY MOBILE. THEIR ATOMIC PARAMETERS ARE DIFFICULT TO REFINE ACCURATELY. THE ...Details: REFINEMENT TOOK PLACE OVER A PERIOD OF MORE THAN 20 YEARS. SOME RESIDUES ARE APPARENTLY DISORDERED AND CERTAINLY MOBILE. THEIR ATOMIC PARAMETERS ARE DIFFICULT TO REFINE ACCURATELY. THE THERMAL PARAMETERS ARE OFTEN OVER 50A**2 WHICH REFLECTS THE UNCERTAINTY IN POSITION AND THE POSSIBILITY OF DISORDER.
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Displacement parameters | Biso mean: 31.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.498→40 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor all: 0.178 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |