1f6l: Difference between revisions

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<StructureSection load='1f6l' size='340' side='right'caption='[[1f6l]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
<StructureSection load='1f6l' size='340' side='right'caption='[[1f6l]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1f6l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F6L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F6L FirstGlance]. <br>
<table><tr><td colspan='2'>[[1f6l]] is a 1 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=1F6L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F6L FirstGlance]. <br>
</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=1f6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f6l OCA], [https://pdbe.org/1f6l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f6l RCSB], [https://www.ebi.ac.uk/pdbsum/1f6l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f6l ProSAT]</span></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</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=1f6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f6l OCA], [https://pdbe.org/1f6l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f6l RCSB], [https://www.ebi.ac.uk/pdbsum/1f6l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f6l ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/KV139_HUMAN KV139_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:20176268, PubMed:17576170).<ref>PMID:17576170</ref> <ref>PMID:20176268</ref> <ref>PMID:22158414</ref> <ref>PMID:24600447</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=1f6l ConSurf].
</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=1f6l ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The antiferritin variable light domain (VL) dimer binds human spleen ferritin ( approximately 85% L subunits) but with approximately 50-fold lower affinity, K(a)=4 x 10(7) x M(-1), than the parent F11 antibody (K(a)=2.1 x 10(9) x M(-1)). The VL dimer does not recognize either rL (100% L subunits) or rH (100% H subunits) human ferritin, whereas the parent antibody recognizes rL-ferritin. To help explain the differences in ferritin binding affinities and specificities, the crystal structure of the VL domain (2.8A resolution) was determined by molecular replacement and models of the antiferritin VL-VH dimer were made on the basis of antilysozyme antibody D1.3. The domain interface is smaller in the VL dimer but a larger number of interdomain hydrogen bonds may prevent rearrangement on antigen binding. The antigen binding surface of the VL dimer is flatter, lacking a negatively charged pocket found in the VL-VH models, contributed by the CDR3 loop of the VH domain. Loop CDR2 (VL dimer) is located away from the antigen binding site, while the corresponding loop of the VH domain would be located within the antigen binding site. Together these differences lead to 50-fold lower binding affinity in the VL dimer and to more restricted specificity than is seen for the parent antibody.
Antiferritin VL homodimer binds human spleen ferritin with high specificity.,Nymalm Y, Kravchuk Z, Salminen T, Chumanevich AA, Dubnovitsky AP, Kankare J, Pentikainen O, Lehtonen J, Arosio P, Martsev S, Johnson MS J Struct Biol. 2002 Jun;138(3):171-86. PMID:12217656<ref>PMID:12217656</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1f6l" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Human]]
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Arosio, P]]
[[Category: Arosio P]]
[[Category: Chumanevich, A A]]
[[Category: Chumanevich AA]]
[[Category: Dubnovitsky, A P]]
[[Category: Dubnovitsky AP]]
[[Category: Johnson, M S]]
[[Category: Johnson MS]]
[[Category: Kankare, J]]
[[Category: Kankare J]]
[[Category: Kravchuk, Z]]
[[Category: Kravchuk Z]]
[[Category: Lehtonen, J]]
[[Category: Lehtonen J]]
[[Category: Martsev, S]]
[[Category: Martsev S]]
[[Category: Nymalm, Y]]
[[Category: Nymalm Y]]
[[Category: Pentikainen, O]]
[[Category: Pentikainen O]]
[[Category: Salminen, T]]
[[Category: Salminen T]]
[[Category: Anti-ferritin antibody]]
[[Category: Dimer]]
[[Category: Immune system]]
[[Category: Immunoglobulin fold]]
[[Category: Variable light chain]]
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