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Open data
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Basic information
Entry | Database: PDB / ID: 9ins | ||||||
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Title | MONOVALENT CATION BINDING IN CUBIC INSULIN CRYSTALS | ||||||
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![]() | HORMONE | ||||||
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 | ![]() | ||||||
![]() | Badger, J. / Dodson, G.G. | ||||||
![]() | ![]() Title: Monovalent cation binding to cubic insulin crystals Authors: Gursky, O. / Li, Y. / Badger, J. / Caspar, D.L.D. #1: ![]() Title: Structure of the Pig Insulin Dimer in the Cubic Crystal Authors: Badger, J. / Harris, M.R. / Reynolds, C.D. / Evans, A.C. / Dodson, E.J. / Dodson, G.G. / North, A.C.T. #2: ![]() Title: Water Structure in Cubic Insulin Crystals Authors: Badger, J. / Caspar, D.L.D. #3: ![]() Title: Zinc-Free Cubic Pig Insulin: Crystallization and Structure Determination Authors: Dodson, E.J. / Dodson, G.G. / Lewitova, A. / Sabesan, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 19.8 KB | Display | ![]() |
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PDB format | ![]() | 15.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418.3 KB | Display | ![]() |
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Full document | ![]() | 420.1 KB | Display | |
Data in XML | ![]() | 5.9 KB | Display | |
Data in CIF | ![]() | 7.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Atom site foot note | 1: WATER 24 IS PROBABLY A PARTIALLY OCCUPIED SODIUM ION. ANOTHER SODIUM SITE WITH VERY LOW OCCUPANCY OVERLAPS THE MAJOR CONFORMATION OF HIS B10 (SEE REF 3). 2: SEE REMARK 5. | |||||||||
Components on special symmetry positions |
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Components
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein/peptide | Mass: 3403.927 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.21 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: microdialysis | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.7→10 Å / Rfactor obs: 0.178 / σ(F): 2 Details: BY COMPARISON WITH MULTIPLE DATA SETS FROM BOVINE CUBIC INSULIN COLLECTED IN THE PH RANGE 7 TO 11 (REFERENCE 1 AND UNPUBLISHED RESULTS) IT HAS BEEN POSSIBLE TO RELIABLY IDENTIFY ADDITIONAL ...Details: BY COMPARISON WITH MULTIPLE DATA SETS FROM BOVINE CUBIC INSULIN COLLECTED IN THE PH RANGE 7 TO 11 (REFERENCE 1 AND UNPUBLISHED RESULTS) IT HAS BEEN POSSIBLE TO RELIABLY IDENTIFY ADDITIONAL CONFORMATIONS FOR SEVERAL SIDE CHAINS THAT WERE NOT INCLUDED IN THE PUBLISHED (ACTA CRYSTALLOGR.) REPORT. THESE HAVE BEEN MODELED, THE ORDERED SOLVENT RATIONALIZED AND THE STRUCTURE REFINED FURTHER. THE R-FACTOR AND STEREOCHEMICAL PARAMETERS IN THIS ENTRY ARE FOR THIS NEW MODEL. IN THE ACTA CRYSTALLOGRAPHICA 1991 PUBLICATION (REFERENCE 2 ABOVE) REFERENCE IS MADE TO PROTEIN DATA BANK ENTRY 5INS. THE COORDINATES IN THIS ENTRY SUPERSEDE 5INS. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rwork: 0.178 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |