2i24: Difference between revisions
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==Crystal structure analysis of the nurse shark New Antigen Receptor PBLA8 variable domain== | ==Crystal structure analysis of the nurse shark New Antigen Receptor PBLA8 variable domain== | ||
<StructureSection load='2i24' size='340' side='right' caption='[[2i24]], [[Resolution|resolution]] 1.35Å' scene=''> | <StructureSection load='2i24' size='340' side='right'caption='[[2i24]], [[Resolution|resolution]] 1.35Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2i24]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2i24]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ginglymostoma_cirratum Ginglymostoma cirratum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I24 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I24 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.35Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2i24 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i24 OCA], [https://pdbe.org/2i24 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i24 RCSB], [https://www.ebi.ac.uk/pdbsum/2i24 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i24 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q8AXH5_GINCI Q8AXH5_GINCI] | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i2/2i24_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i2/2i24_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/ | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=2i24 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 25: | Line 28: | ||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 2i24" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
| Line 30: | Line 34: | ||
</StructureSection> | </StructureSection> | ||
[[Category: Ginglymostoma cirratum]] | [[Category: Ginglymostoma cirratum]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Stanfield RL]] | ||
[[Category: | [[Category: Wilson IA]] | ||
Latest revision as of 08:16, 17 October 2024
Crystal structure analysis of the nurse shark New Antigen Receptor PBLA8 variable domainCrystal structure analysis of the nurse shark New Antigen Receptor PBLA8 variable domain
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedSharks express an unusual heavy-chain isotype called IgNAR, whose variable regions bind antigen as independent soluble domains. To further probe affinity maturation of the IgNAR response, we structurally characterized the germline and somatically matured versions of a type II variable (V) region, both in the presence and absence of its antigen, hen egg-white lysozyme. Despite a disulfide bond linking complementarity determining regions (CDRs) 1 and 3, both germline and somatically matured V regions displayed significant structural changes in these CDRs upon complex formation with antigen. Somatic mutations in the IgNAR V region serve to increase the number of contacts with antigen, as reflected by a tenfold increase in affinity, and one of these mutations appears to stabilize the CDR3 region. In addition, a residue in the HV4 loop plays an important role in antibody-antigen interaction, consistent with the high rate of somatic mutations in this non-CDR loop. Maturation of shark single-domain (IgNAR) antibodies: evidence for induced-fit binding.,Stanfield RL, Dooley H, Verdino P, Flajnik MF, Wilson IA J Mol Biol. 2007 Mar 23;367(2):358-72. Epub 2006 Dec 22. PMID:17258766[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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