1r70: Difference between revisions

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 ==Model of human IgA2 determined by solution scattering, curve fitting and homology modelling==
-<StructureSection load='1r70' size='340' side='right' caption='[[1r70]], [[Resolution|resolution]] 30.00&Aring;' scene=''>
+<StructureSection load='1r70' size='340' side='right'caption='[[1r70]], [[Resolution|resolution]] 30.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1r70]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R70 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1R70 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1r70]] is a 4 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=1R70 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R70 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1vge|1vge]], [[2fbj|2fbj]], [[1fc1|1fc1]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray solution scattering, [[Resolution|Resolution]] 30&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">human alpha 2 gene (light chain) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), human alpha 2 gene (heavy chain) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=1r70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r70 OCA], [https://pdbe.org/1r70 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r70 RCSB], [https://www.ebi.ac.uk/pdbsum/1r70 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r70 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1r70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r70 OCA], [http://pdbe.org/1r70 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1r70 RCSB], [http://www.ebi.ac.uk/pdbsum/1r70 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1r70 ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 12: / Line 11: @@
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r7/1r70_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r7/1r70_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 18: / Line 17: @@
 </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=1r70 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Immunoglobulin A (IgA), the most abundant human immunoglobulin, mediates immune protection at mucosal surfaces as well as in plasma. It exists as two subclasses IgA1 and IgA2, and IgA2 is found in at least two allotypic forms, IgA2m(1) or IgA2m(2). Compared to IgA1, IgA2 has a much shorter hinge region, which joins the two Fab and one Fc fragments. In order to assess its solution structure, monomeric recombinant IgA2m(1) was studied by X-ray and neutron scattering. Its Guinier X-ray radius of gyration R(G) is 5.18 nm and its neutron R(G) is 5.03 nm, both of which are significantly smaller than those for monomeric IgA1 at 6.1-6.2 nm. The distance distribution function P(r)for IgA2m(1) showed a broad peak with a subpeak and gave a maximum dimension of 17 nm, in contrast to the P(r) curve for IgA1, which showed two distinct peaks and a maximum dimension of 21 nm. The sedimentation coefficients of IgA1 and IgA2m(1) were 6.2S and 6.4S, respectively. These data show that the solution structure of IgA2m(1) is significantly more compact than IgA1. The complete monomeric IgA2m(1) structure was modelled using molecular dynamics to generate random IgA2 hinge structures, to which homology models for the Fab and Fc fragments were connected to generate 10,000 full models. A total of 104 compact best-fit IgA2m(1) models gave good curve fits. These best-fit models were modified by linking the two Fab light chains with a disulphide bridge that is found in IgA2m(1), and subjecting these to energy refinement to optimise this linkage. The averaged solution structure of the arrangement of the Fab and Fc fragments in IgA2m(1) was found to be predominantly T-shaped and flexible, but also included Y-shaped structures. The IgA2 models show full steric access to the two FcalphaRI-binding sites at the Calpha2-Calpha3 interdomain region in the Fc fragment. Since previous scattering modelling had shown that IgA1 also possessed a flexible T-shaped solution structure, such a T-shape may be common to both IgA1 and IgA2. The final models suggest that the combination of the more compact IgA2m(1) and the more extended IgA1 structures will enable human IgA to access a broader range of antigens than either acting alone. The hinges of both IgA subclasses appear to show reduced flexibility when compared to their equivalents in IgG, and this may be important for maintaining an extended IgA structure.
-Solution structure determination of monomeric human IgA2 by X-ray and neutron scattering, analytical ultracentrifugation and constrained modelling: a comparison with monomeric human IgA1.,Furtado PB, Whitty PW, Robertson A, Eaton JT, Almogren A, Kerr MA, Woof JM, Perkins SJ J Mol Biol. 2004 May 14;338(5):921-41. PMID:15111057<ref>PMID:15111057</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1r70" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[IgA|IgA]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Almogren, A]]
+[[Category: Large Structures]]
-[[Category: Eaton, J T]]
+[[Category: Almogren A]]
-[[Category: Furtado, P B]]
+[[Category: Eaton JT]]
-[[Category: Kerr, M A]]
+[[Category: Furtado PB]]
-[[Category: Perkins, S J]]
+[[Category: Kerr MA]]
-[[Category: Robertson, A]]
+[[Category: Perkins SJ]]
-[[Category: Whitty, P W]]
+[[Category: Robertson A]]
-[[Category: Woof, J M]]
+[[Category: Whitty PW]]
-[[Category: Antibody]]
+[[Category: Woof JM]]
-[[Category: Glycoprotein]]
-[[Category: Ig fold]]
-[[Category: Iga]]
-[[Category: Immune system]]
-[[Category: Immunology]]