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Open data
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Basic information
Entry | Database: PDB / ID: 1zni | ||||||
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Title | INSULIN | ||||||
![]() | (INSULIN) x 2 | ||||||
![]() | HORMONE / GLUCOSE METABOLISM | ||||||
Function / homology | ![]() 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 / positive regulation of fatty acid biosynthetic process / positive regulation of glucose metabolic process / lipoprotein biosynthetic process / COPI-mediated anterograde transport / lipid biosynthetic process / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of protein autophosphorylation / positive regulation of DNA replication / positive regulation of protein secretion / insulin-like growth factor receptor binding / insulin receptor binding / hormone activity / glucose metabolic process / insulin receptor signaling pathway / glucose homeostasis / positive regulation of cell migration / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Turkenburg, M.G.W. / Whittingham, J.L. / Dodson, G.G. / Dodson, E.J. / Xiao, B. / Bentley, G.A. | ||||||
![]() | ![]() Title: Structure of insulin in 4-zinc insulin. Authors: Bentley, G. / Dodson, E. / Dodson, G. / Hodgkin, D. / Mercola, D. #1: ![]() Title: The Structure of a Rhombohedral R6 Insulin Hexamer that Binds Phenol Authors: Smith, G.D. / Dodson, G.G. #2: ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() Title: Rhombohedral Insulin Crystal Transformation Authors: Bentley, G. / Dodson, G. / Lewitova, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 33.6 KB | Display | ![]() |
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PDB format | ![]() | 26.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 379.7 KB | Display | ![]() |
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Full document | ![]() | 382.9 KB | Display | |
Data in XML | ![]() | 4.2 KB | Display | |
Data in CIF | ![]() | 6.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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5 | ![]()
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7 | ![]()
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8 | ![]()
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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. | |
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Components
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein/peptide | Mass: 3403.927 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #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: ![]() |
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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 |
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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 |