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Yorodumi- PDB-4ins: THE STRUCTURE OF 2ZN PIG INSULIN CRYSTALS AT 1.5 ANGSTROMS RESOLUTION -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ins | |||||||||
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Title | THE STRUCTURE OF 2ZN PIG INSULIN CRYSTALS AT 1.5 ANGSTROMS RESOLUTION | |||||||||
Components |
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Keywords | HORMONE | |||||||||
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 / positive regulation of fatty acid biosynthetic process / positive regulation of glucose metabolic process / lipoprotein biosynthetic process / COPI-mediated anterograde transport / lipid biosynthetic process / positive regulation of DNA replication / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / positive regulation of protein secretion / hormone activity / glucose metabolic process / glucose homeostasis / insulin receptor signaling pathway / positive regulation of cell migration / extracellular space / identical protein binding Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.5 Å | |||||||||
Authors | Dodson, G.G. / Dodson, E.J. / Hodgkin, D.C. / Isaacs, N.W. / Vijayan, M. | |||||||||
Citation | 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. #1: Journal: Proc.R.Soc.London,Ser.B / Year: 1983 Title: A Comparative Assessment of the Zinc-Protein Coordination in 2Zn-Insulin as Determined by X-Ray Absorption Fine Structure (Exafs) and X-Ray Crystallography Authors: Bordas, J. / Dodson, G.G. / Grewe, H. / Koch, M.H.J. / Krebs, B. / Randall, J. #2: Journal: Can.J.Biochem. / Year: 1979 Title: Structural Relationships in the Two-Zinc Insulin Hexamer Authors: Dodson, E.J. / Dodson, G.G. / Hodgkin, D.C. / Reynolds, C.D. #3: Journal: Acta Crystallogr.,Sect.A / Year: 1978 Title: Experience with Fast Fourier Least Squares in the Refinement of the Crystal Structure of Rhombohedral 2-Zinc Insulin at 1.5 Angstroms Resolution Authors: Isaacs, N.W. / Agarwal, R.C. #4: Journal: J.Mol.Biol. / Year: 1978 Title: Rhombohedral Insulin Crystal Transformation Authors: Bentley, G. / Dodson, G. / Lewitova, A. #5: Journal: Acta Crystallogr.,Sect.A / Year: 1976 Title: A Method for Fitting Satisfactory Models to Sets of Atomic Positions in Protein Structure Refinements Authors: Dodson, E.J. / Isaacs, N.W. / Rollett, J.S. #8: Journal: Adv.Protein Chem. / Year: 1972 Title: Insulin. The Structure in the Crystal and its Reflection in Chemistry and Biology Authors: Blundell, T. / Dodson, G. / Hodgkin, D. / Mercola, D. #9: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972 Title: The Crystal Structure of Rhombohedral 2 Zinc Insulin Authors: Blundell, T.L. / Cutfield, J.F. / Dodson, E.J. / Dodson, G.G. / Hodgkin, D.C. / Mercola, D.A. #10: Journal: Nature / Year: 1971 Title: Atomic Positions in Rhombohedral 2-Zinc Insulin Crystals Authors: Blundell, T.L. / Cutfield, J.F. / Cutfield, S.M. / Dodson, E.J. / Dodson, G.G. / Hodgkin, D.C. / Mercola, D.A. / Vijayan, M. #11: Journal: Recent Prog.Horm.Res. / Year: 1971 Title: X-Ray Analysis and the Structure of Insulin Authors: Blundell, T.L. / Dodson, G.G. / Dodson, E. / Hodgkin, D.C. / Vijayan, M. #12: Journal: J.Mol.Biol. / Year: 1970 Title: X-Ray Diffraction Data on Some Crystalline Varieties of Insulin Authors: Baker, E.N. / Dodson, G. #13: Journal: Nature / Year: 1969 Title: Structure of Rhombohedral 2 Zinc Insulin Crystals Authors: Adams, M.J. / Blundell, T.L. / Dodson, E.J. / Dodson, G.G. / Vijayan, M. / Baker, E.N. / Harding, M.M. / Hodgkin, D.C. / Rimmer, B. / Sheat, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ins.cif.gz | 40.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ins.ent.gz | 30.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ins.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ins_validation.pdf.gz | 383.5 KB | Display | wwPDB validaton report |
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Full document | 4ins_full_validation.pdf.gz | 388.7 KB | Display | |
Data in XML | 4ins_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | 4ins_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/4ins ftp://data.pdbj.org/pub/pdb/validation_reports/in/4ins | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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5 |
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6 |
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7 |
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Unit cell |
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Atom site foot note | 1: THE QUASI-TWO-FOLD SYMMETRY BREAKS DOWN MOST SERIOUSLY AT RESIDUES GLY A 1 TO GLN A 5 AND GLY C 1 TO GLN C 5 HIS B 5 AND HIS D 5 PHE B 25 AND PHE D 25 2: THE FOLLOWING RESIDUES ARE DISORDERED - GLN B 4, VAL B 12, GLU B 21, ARG B 22, ARG D 22, LYS D 29. 3: SEE REMARK 8. | ||||||||||||||||||||||||
Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.87862, -0.47696, 0.02305), Details | THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT OF INSULIN CONSISTS OF TWO INSULIN MOLECULES EACH CONSISTING OF TWO CHAINS. THIS ENTRY PRESENTS COORDINATES FOR MOLECULES I (CHAIN INDICATORS *A* AND *B*) AND II (CHAIN INDICATORS *C* AND *D*). THE QUASI-TWO-FOLD AXIS THAT TRANSFORMS MOLECULE I INTO MOLECULE II IS GIVEN IN THE *MTRIX* RECORDS BELOW. 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 BELOW WITH A BLANK CHAIN INDICATOR. | |
-Components
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P01315 #2: Protein/peptide | Mass: 3403.927 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P01315 #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.05 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.2 / Method: unknown | ||||||||||||||||||||||||||||||
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 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||
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Refinement | Rfactor obs: 0.153 / Highest resolution: 1.5 Å Details: SOME RESIDUES ARE APPARENTLY DISORDERED BUT DIFFICULT TO DESCRIBE IN TERMS OF ATOMIC POSITIONS. ALA B 30 IS ONE OF THESE RESIDUES. THE FOLLOWING RESIDUES ARE DISORDERED - GLN B 4, VAL B 12, ...Details: SOME RESIDUES ARE APPARENTLY DISORDERED BUT DIFFICULT TO DESCRIBE IN TERMS OF ATOMIC POSITIONS. ALA B 30 IS ONE OF THESE RESIDUES. THE FOLLOWING RESIDUES ARE DISORDERED - GLN B 4, VAL B 12, GLU B 21, ARG B 22, ARG D 22, LYS D 29. | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.5 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 10119 / σ(I): 2 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |