3cdy

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{{Seed}}
 
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[[Image:3cdy.png|left|200px]]
 
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==AL-09 H87Y, immunoglobulin light chain variable domain==
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The line below this paragraph, containing "STRUCTURE_3cdy", creates the "Structure Box" on the page.
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<StructureSection load='3cdy' size='340' side='right'caption='[[3cdy]], [[Resolution|resolution]] 2.43&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3cdy]] is a 2 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=3CDY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CDY FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.43&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3cdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cdy OCA], [https://pdbe.org/3cdy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cdy RCSB], [https://www.ebi.ac.uk/pdbsum/3cdy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cdy ProSAT]</span></td></tr>
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{{STRUCTURE_3cdy| PDB=3cdy | SCENE= }}
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/KV133_HUMAN KV133_HUMAN] V region of the variable domain of immunoglobulin light chains that participates in the antigen recognition (PubMed:24600447). Immunoglobulins, also known as antibodies, are membrane-bound or secreted glycoproteins produced by B lymphocytes. In the recognition phase of humoral immunity, the membrane-bound immunoglobulins serve as receptors which, upon binding of a specific antigen, trigger the clonal expansion and differentiation of B lymphocytes into immunoglobulins-secreting plasma cells. Secreted immunoglobulins mediate the effector phase of humoral immunity, which results in the elimination of bound antigens (PubMed:20176268, PubMed:22158414). The antigen binding site is formed by the variable domain of one heavy chain, together with that of its associated light chain. Thus, each immunoglobulin has two antigen binding sites with remarkable affinity for a particular antigen. The variable domains are assembled by a process called V-(D)-J rearrangement and can then be subjected to somatic hypermutations which, after exposure to antigen and selection, allow affinity maturation for a particular antigen (PubMed:17576170, PubMed:20176268).<ref>PMID:17576170</ref> <ref>PMID:20176268</ref> <ref>PMID:22158414</ref> <ref>PMID:24600447</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cd/3cdy_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3cdy ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Mechanisms of amyloidogenesis are not well understood, including potential structural contributions of mutations in the process. Our previous research indicated that the dimer interface of amyloidogenic immunoglobulin light chain protein AL-09 is twisted 90 degrees relative to the protein from its germline sequence, kappaI O18/O8. Here we report a systematic restoration of AL-09 to its germline sequence by mutating the non-conservative somatic mutations located in the light chain dimer interface. Among these mutants, we find a correlation between increased thermodynamic stability and an increase in the lag time for fibril formation. The restorative mutant AL-09 H87Y completes the trifecta and restores the dimer interface observed in kappaI O18/O8, emphasizing the potential importance of the structural integrity of these proteins to protect against amyloidogenicity. We also find that adding amyloidogenic mutations into the germline protein illustrates mutational cooperativity in promoting amyloidogenesis.
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===AL-09 H87Y, immuglobulin light chain variable domain===
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Structural insights into the role of mutations in amyloidogenesis.,Baden EM, Randles EG, Aboagye AK, Thompson JR, Ramirez-Alvarado M J Biol Chem. 2008 Nov 7;283(45):30950-6. Epub 2008 Sep 2. PMID:18768467<ref>PMID:18768467</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_18768467}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3cdy" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 18768467 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18768467}}
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__TOC__
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</StructureSection>
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==About this Structure==
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3CDY is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CDY OCA].
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==Reference==
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<ref group="xtra">PMID:18768467</ref><references group="xtra"/>
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Aboagye, A K.]]
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[[Category: Large Structures]]
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[[Category: Baden, E M.]]
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[[Category: Aboagye AK]]
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[[Category: Ramirez-Alvarado, M.]]
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[[Category: Baden EM]]
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[[Category: Randles, E G.]]
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[[Category: Ramirez-Alvarado M]]
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[[Category: Thompson, J R.]]
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[[Category: Randles EG]]
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[[Category: Amyloidosis]]
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[[Category: Thompson JR]]
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[[Category: Greek key beta barrel]]
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[[Category: Immune system]]
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[[Category: Immunoglobulin]]
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[[Category: Light chain]]
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[[Category: Variable domain]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:19:03 2009''
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Current revision

AL-09 H87Y, immunoglobulin light chain variable domain

PDB ID 3cdy

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