2omg: Difference between revisions

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-[[Image:2omg.gif|left|200px]]<br />
-<applet load="2omg" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2omg, resolution 1.52&Aring;" />
-'''Structure of human insulin cocrystallized with protamine and urea'''<br />
-==Overview==
+==Structure of human insulin cocrystallized with protamine and urea==
-Insulin NPH (neutral protamine hagedorn) has for long been one of the most, important therapeutic formulations for the treatment of diabetes. The, protracted action profile of NPH formulations is gained from crystallizing, insulin with zinc in the presence of the basic poly-arginine peptide, protamine. In spite of its long history and successful use, the binding, mode of the insulin-protamine complex is not known. In this study, three, different systems were used to study protamine binding to insulin. In the, first system, crystals of an insulin-protamine complex grown in the, presence of urea and diffracting to 1.5A resolution were analyzed. In the, second system, a shorter peptide consisting of 12 arginine residues was, co-crystallized with insulin in order to reduce the flexibility and, thereby improve the electron density of the peptide. Both systems yielded, data to a significantly higher resolution than obtained previously. In, addition, a third system was analyzed where crystals of insulin and, protamine were grown in the absence of urea, with conditions closely, resembling the pharmaceutical formulation. Data from these NPH, microcrystals could for the first time be collected to 2.2A resolution at, a micro focused X-ray beamline. Analysis of all three crystal forms reveal, potential protamine density located close to the solvent channel leading, to the centrally located zinc atoms in the insulin hexamer and support, that protamine binds to insulin in a not well defined conformation.
+<StructureSection load='2omg' size='340' side='right'caption='[[2omg]], [[Resolution|resolution]] 1.52&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2omg]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OMG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OMG FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.52&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CRS:M-CRESOL'>CRS</scene>, <scene name='pdbligand=EJJ:2-(aminocarbonylamino)ethanoic+acid'>EJJ</scene>, <scene name='pdbligand=ING:D-[(AMINO)CARBONYL]PHENYLALANINE'>ING</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=URE:UREA'>URE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2omg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2omg OCA], [https://pdbe.org/2omg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2omg RCSB], [https://www.ebi.ac.uk/pdbsum/2omg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2omg ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/INS_HUMAN INS_HUMAN] Defects in INS are the cause of familial hyperproinsulinemia (FHPRI) [MIM:[https://omim.org/entry/176730 176730].<ref>PMID:3470784</ref> <ref>PMID:2196279</ref> <ref>PMID:4019786</ref> <ref>PMID:1601997</ref>   Defects in INS are a cause of diabetes mellitus insulin-dependent type 2 (IDDM2) [MIM:[https://omim.org/entry/125852 125852]. IDDM2 is a multifactorial disorder of glucose homeostasis that is characterized by susceptibility to ketoacidosis in the absence of insulin therapy. Clinical fetaures are polydipsia, polyphagia and polyuria which result from hyperglycemia-induced osmotic diuresis and secondary thirst. These derangements result in long-term complications that affect the eyes, kidneys, nerves, and blood vessels.<ref>PMID:18192540</ref>   Defects in INS are a cause of diabetes mellitus permanent neonatal (PNDM) [MIM:[https://omim.org/entry/606176 606176]. PNDM is a rare form of diabetes distinct from childhood-onset autoimmune diabetes mellitus type 1. It is characterized by insulin-requiring hyperglycemia that is diagnosed within the first months of life. Permanent neonatal diabetes requires lifelong therapy.<ref>PMID:17855560</ref> <ref>PMID:18162506</ref>   Defects in INS are a cause of maturity-onset diabetes of the young type 10 (MODY10) [MIM:[https://omim.org/entry/613370 613370]. MODY10 is a form of diabetes that is characterized by an autosomal dominant mode of inheritance, onset in childhood or early adulthood (usually before 25 years of age), a primary defect in insulin secretion and frequent insulin-independence at the beginning of the disease.<ref>PMID:18192540</ref> <ref>PMID:18162506</ref> <ref>PMID:20226046</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/INS_HUMAN INS_HUMAN] Insulin decreases blood glucose concentration. It increases cell permeability to monosaccharides, amino acids and fatty acids. It accelerates glycolysis, the pentose phosphate cycle, and glycogen synthesis in liver.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/om/2omg_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2omg ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Insulin NPH (neutral protamine hagedorn) has for long been one of the most important therapeutic formulations for the treatment of diabetes. The protracted action profile of NPH formulations is gained from crystallizing insulin with zinc in the presence of the basic poly-arginine peptide protamine. In spite of its long history and successful use, the binding mode of the insulin-protamine complex is not known. In this study, three different systems were used to study protamine binding to insulin. In the first system, crystals of an insulin-protamine complex grown in the presence of urea and diffracting to 1.5A resolution were analyzed. In the second system, a shorter peptide consisting of 12 arginine residues was co-crystallized with insulin in order to reduce the flexibility and thereby improve the electron density of the peptide. Both systems yielded data to a significantly higher resolution than obtained previously. In addition, a third system was analyzed where crystals of insulin and protamine were grown in the absence of urea, with conditions closely resembling the pharmaceutical formulation. Data from these NPH microcrystals could for the first time be collected to 2.2A resolution at a micro focused X-ray beamline. Analysis of all three crystal forms reveal potential protamine density located close to the solvent channel leading to the centrally located zinc atoms in the insulin hexamer and support that protamine binds to insulin in a not well defined conformation.
-==Disease==
+Structural characterization of insulin NPH formulations.,Norrman M, Hubalek F, Schluckebier G Eur J Pharm Sci. 2007 Apr;30(5):414-23. Epub 2007 Jan 20. PMID:17339105<ref>PMID:17339105</ref>
-Known diseases associated with this structure: Diabetes mellitus, rare form OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=176730 176730]], Hyperproinsulinemia, familial OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=176730 176730]], MODY, one form OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=176730 176730]]
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-OMG is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with ZN, CL, NA, CRS, URE and ARF as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2OMG OCA].
+</div>
+<div class="pdbe-citations 2omg" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structural characterization of insulin NPH formulations., Norrman M, Hubalek F, Schluckebier G, Eur J Pharm Sci. 2007 Apr;30(5):414-23. Epub 2007 Jan 20. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17339105 17339105]
+*[[Insulin 3D Structures|Insulin 3D Structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Norrman, M.]]
+[[Category: Norrman M]]
-[[Category: Schluckebier, G.]]
+[[Category: Schluckebier G]]
-[[Category: ARF]]
-[[Category: CL]]
-[[Category: CRS]]
-[[Category: NA]]
-[[Category: URE]]
-[[Category: ZN]]
-[[Category: insulin nph like crystal]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 23:13:01 2007''