3eba: Difference between revisions

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-{{Seed}}
-[[Image:3eba.png|left|200px]]
-<!--
+==CAbHul6 FGLW mutant (humanized) in complex with human lysozyme==
-The line below this paragraph, containing "STRUCTURE_3eba", creates the "Structure Box" on the page.
+<StructureSection load='3eba' size='340' side='right'caption='[[3eba]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3eba]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Camelus_dromedarius Camelus dromedarius] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EBA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EBA FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3eba|  PDB=3eba  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3eba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eba OCA], [https://pdbe.org/3eba PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eba RCSB], [https://www.ebi.ac.uk/pdbsum/3eba PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eba ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/LYSC_HUMAN LYSC_HUMAN] Defects in LYZ are a cause of amyloidosis type 8 (AMYL8) [MIM:[https://omim.org/entry/105200 105200]; also known as systemic non-neuropathic amyloidosis or Ostertag-type amyloidosis. AMYL8 is a hereditary generalized amyloidosis due to deposition of apolipoprotein A1, fibrinogen and lysozyme amyloids. Viscera are particularly affected. There is no involvement of the nervous system. Clinical features include renal amyloidosis resulting in nephrotic syndrome, arterial hypertension, hepatosplenomegaly, cholestasis, petechial skin rash.<ref>PMID:8464497</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/LYSC_HUMAN LYSC_HUMAN] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents.
+== 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/eb/3eba_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=3eba ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Nanobodies, single-domain antigen-binding fragments of camelid-specific heavy-chain only antibodies offer special advantages in therapy over classic antibody fragments because of their smaller size, robustness, and preference to target unique epitopes. A Nanobody differs from a human heavy chain variable domain in about ten amino acids spread all over its surface, four hallmark Nanobody-specific amino acids in the framework-2 region (positions 42, 49, 50, and 52), and a longer third antigen-binding loop (H3) folding over this area. For therapeutic applications the camelid-specific amino acid sequences in the framework have to be mutated to their human heavy chain variable domain equivalent, i.e. humanized. We performed this humanization exercise with Nanobodies of the subfamily that represents close to 80% of all dromedary-derived Nanobodies and investigated the effects on antigen affinity, solubility, expression yield, and stability. It is demonstrated that the humanization of Nanobody-specific residues outside framework-2 are neutral to the Nanobody properties. Surprisingly, the Glu-49 --&gt; Gly and Arg-50 --&gt; Leu humanization of hallmark amino acids generates a single domain that is more stable though probably less soluble. The other framework-2 substitutions, Phe-42 --&gt; Val and Gly/Ala-52 --&gt; Trp, are detrimental for antigen affinity, due to a repositioning of the H3 loop as shown by their crystal structures. These insights were used to identify a soluble, stable, well expressed universal humanized Nanobody scaffold that allows grafts of antigen-binding loops from other Nanobodies with transfer of the antigen specificity and affinity.
-===CAbHul6 FGLW mutant (humanized) in complex with human lysozyme===
+General strategy to humanize a camelid single-domain antibody and identification of a universal humanized nanobody scaffold.,Vincke C, Loris R, Saerens D, Martinez-Rodriguez S, Muyldermans S, Conrath K J Biol Chem. 2009 Jan 30;284(5):3273-84. Epub 2008 Nov 14. PMID:19010777<ref>PMID:19010777</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3eba" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19010777}}, adds the Publication Abstract to the page
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19010777 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19010777}}
+__TOC__
+</StructureSection>
-==About this Structure==
-EBA is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Camelus_dromedarius Camelus dromedarius] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EBA OCA].
-==Reference==
-<ref group="xtra">PMID:19010777</ref><references group="xtra"/>
 [[Category: Camelus dromedarius]]
 [[Category: Homo sapiens]]
-[[Category: Lysozyme]]
+[[Category: Large Structures]]
-[[Category: Conrath, K.]]
+[[Category: Conrath K]]
-[[Category: Loris, R.]]
+[[Category: Loris R]]
-[[Category: Martinez-Rodriguez, S.]]
+[[Category: Martinez-Rodriguez S]]
-[[Category: Muyldermans, S.]]
+[[Category: Muyldermans S]]
-[[Category: Saerens, D.]]
+[[Category: Saerens D]]
-[[Category: Vincke, C.]]
+[[Category: Vincke C]]
-[[Category: Amyloid]]
-[[Category: Amyloid fibril formation inhibition]]
-[[Category: Antigen-antibody complex]]
-[[Category: Antimicrobial]]
-[[Category: Bacteriolytic enzyme]]
-[[Category: Disease mutation]]
-[[Category: Glycosidase]]
-[[Category: Humanization]]
-[[Category: Hydrolase]]
-[[Category: Immune system/hydrolase complex]]
-[[Category: Immunoglobulin]]
-[[Category: Nanobody]]
-[[Category: Polymorphism]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 15 08:47:50 2009''